Never apologize; asking questions is how we learn things.
Here's a bit of history - in reverse.
Most modern gear has a separate headphone amp for its headphone output.
This may be made out of several discrete transistors, just like a little power amp, or it may all be in an integrated circuit - usually the latter.
These little amps are usually very quiet, very low in distortion, and, since they're connected directly to the headphones, they provide pretty good damping.
Also, because of that low output impedance, they don't interact with the headphones - the amp itself sounds the same with different headphone models.
(Output impedances range from very low up to 5 Ohms or so.)
With current parts these little amps only add a few dollars to the cost - so virtually all gear with a separate headphone output uses them.
The only real down-side is that they usually don't have much power or voltage - so they don't do well with high impedance headphones or really low efficiency models.
In contrast, most vintage gear did NOT have a separate amplifier for the headphones.
Back then, parts were more expensive, and there simply wasn't as much interest in headphones.
Therefore, most vintage gear simply connects your headphones to the main speaker outputs through a series dropping resistor.
This requires a single low cost part... so it's easy and cheap.
However, there are several drawbacks to doing it that way.
Speaker outputs usually have more noise and more distortion than a purpose designed headphone amp (and they're both more noticeable with headphones).
The output impedance in that configuration is equal to the value of the series resistor you use - and so is usually quite high (the A-100 is typical at 220 Ohms).
This high output impedance causes two things - both of which affect low impedance headphones more than high impedance ones.
First off, because damping depends on the ratio between the impedance of the amp and the impedance of the headphones, there is MUCH less damping.
Second, the output impedance interacts with the impedance of the headphones.... so the amp has a "slightly different personality" with different models of headphones.
There were several things that motivated us to design the A-100 the way we did.
1) Certain early planar headphones have a very low impedance, and are VERY inefficient, and in fact have needs more like speakers than headphones. This prompted many people to start running them directly from the outputs of a "speaker amplifier" using a special adapter cable. We noticed that many people were using the previous version of the A-100, the Mini-X, that way. (There are only a few models of headphones that really need all that power these days, but many people noticed that there were benefits even with normal high impedance headphones, or with other hard to drive models.)
2) Even though they have some drawbacks, the headphone outputs on vintage equipment have developed a bit of a cult following. Some people LIKE the way they interact with the headphones, so each model has its own characteristic sound on each different amp. (There are whole threads on Head-Fi dedicated to "listening to headphones on vintage gear).
Therefore, we decided to use a "vintage style headphone output" on the A-100.
Here are a few of the details worth noting....
1)
With the jumpers out the A-100 has an output impedance of 220 Ohms.
This means that, like with vintage equipment, it applies very little damping to the headphones (many will sound different because of this - which could be good or bad).
Likewise, the impedance of the amplifier will actually interact with the impedance of the headphones (again, the effect this has will vary with different headphones).
These effects will be major with low impedance headphones and relatively much less with high impedance headphones.
The A-100 will have plenty of voltage to drive even very high impedance headphones very well.
(The A-100 has much less noise and distortion than most vintage equipment - so these are much less of an issue).
2)
With the jumpers IN, the main outputs of the A-100 are connected directly to your headphones.
if you had headphones that had to be connected directly to the speaker outputs on an amplifier - this is the same thing.
With the jumpers IN the gain of the entire system is very high - which means more noise and more power.
(If your headphones are very inefficient, you'll need the power, and you won't notice the noise. With more normal headphones this may be a bad choice.)
Now, just a little bit about how amplifiers work inside.
When the audio signal enters the A-100, it goes through a voltage divider (the Volume control), and then on to what is basically a power amplifier.
The amplifier portion always boosts the voltage by the same amount; the Volume control adjusts the level by cutting down the level of the signal going in.
(This is how virtually all amplifiers with volume controls work.)
Now... if you notice a lot of noise.....
(this is more likely to occur with the jumpers in and the resistors bypassed).
IF the noise remains the same, regardless of where you set the Volume control on the A-100, then you're hearing the internal noise of the A-100's amplifier itself.
If that's the case, then the only way to reduce it is to reduce the level at the OUTPUT - by putting a power attenuator between the output and your headphones.
(Or, if your headphones are very sensitive, perhaps you should try putting the jumpers in, or perhaps you just don't need an amplifier this powerful.)
IF the noise level changes when you adjust the Volume control on the A-100, then that means that the noise is coming in from the previous component.
If that's the case, then putting a line-level attenuator between the previous component and the INPUT of the A-100 will help.
Likewise, if you simply can't turn the Volume control on the A-100 up more than a few degrees, the best solution is an attenuator on the INPUT of the A-100.
Your Topping D10 is a DAC.
Therefore, you are NOT feeding the A-100 audio from your motherboard.
Your Topping D10 has replaced the sound card on your motherboard and is acting in its place.
However,your D10 doesn't have its own volume control, so....
If the noise goes up and down with the Volume setting on the A-100 then you're hearing the noise floor on the output of the Topping.
If that's the case, then putting an attenuator between the Topping and the A-100 should help.
If the noise remains the same, regardless of where you set the Volume on the A-100, then you're hearing the noise floor on the A-100 itself.
If so, then putting an attenuator between the output of the A-100 and your headphones will improve matters.
(But, if that's the case, maybe you should simply consider using a less powerful amplifier with those headphones instead.)
If you put a preamp between your Topping and the A-100 several things will happen.
You will add another opportunity to control the level - which may or may not help in your case.
Whatever noise and distortion this new device creates will be added to whatever is already there.
Tube equipment produces certain types of distortion that some people find pleasing.
Therefore, adding a tube preamp will almost certainly add coloration to the sound.... but you might find it to be pleasant.
If the equalizer software on your computer reports clipping then that will definitely make the sound quality worse...
And it's something that has to be handled on the computer by the player software.
(The computer doesn't know what the DAC or the amp are doing; if it reports clipping then that means that it is the program doing the clipping.)
You could try turning the level on the player software down a bit - and the level on the A-100 up a bit.
The standard advice for best sound quality would be to "run the computer volume at full" and use other Volume controls to lower it.
However, if something in the software is actually clipping, then you should forget that advice, and turn your player software down until it ISN'T clipping.
It's not uncommon for player programs to allow you to choose equalizer settings that may sometimes cause them to clip.
(If the sound files themselves, or the video you're playing, are simply themselves clipped, there's not much you can do about it.)
It's extremely UNLIKELY that speaker wires will make any difference.... unless they're actually frayed or broken.
A LOOSE connection can cause distortion... but is quite unlikely to cause "grounding issues".