Seal and fit is very important. Even slight adjustments to the pads can make a big difference here. I have found the AD to be one of the pickiest headphones when it comes to getting this right. You might also need to adjust the headband for a better fit, as a tight clamp doesn't necessarily imply good fit and seal. I'd also make sure to let the pads warm up and comform to your head with ~10 minutes of listening or so before really judging them. If something sounds off, try playing with the fit and seal to see if you can improve it...really, even the tiniest differences can make or break the sound in the end. Harder to get right for some than you'd expect.
The damping "dots" (squares, rather) applied to the front side of the drivers do a decent job smoothing the upper mid and treble response. If your pair only has one dot per channel, you could consider using two in a bar shaped pattern (middle section, two driver holes visible on top and bottom each). Dan provides those on his, as he mentioned, or you could try creating your own with similar (or not) materials. Similarly, the felt discs are good for tuning the upper end if you want a smoother sound. I generally run 2 discs to smooth out the sound despite trade offs in other areas (smoother and more even but more veiled, less resolving, less air, etc.). The Alpha Dog tends to have two peaks in the 5-6KHz and 9-10KHz areas, and these tweaks assist in smoothing that whole area out for folks that find them unpleasant.
The Alpha Dog does have a touch of extra bass below ~80Hz by default, and harmonic distortion in that area can similarly be a touch elevated depending on your listening levels. I first noticed this when I took measurements (not publicly posted, though perhaps in a future review) and later verified this when Tyll posted his own measurements. Don't get me wrong, the response and distortion numbers are still quite good, but harmonic distortion, especially in the bass, can make bass sound looser, muddier, and give it more rumble than it would in a perfect situation. The harmonic distortion below 100Hz on the Alpha Dog is more on par with something like, say, the HD600 vs. something like the LCD-2, which has extremely low harmonic distortion across the board. Part of this is limitations of the T50RP driver, part of it is the particular AD configuration. The AD is still very good in the end, but that could play a role in what you're perceiving. I sometimes find a touch of extra bass and harmonic distortion down there to be pleasant anyway...extra sense of rumble can sometimes bring that tactile bass feel folks like, though it's more often the case it just sounds bad (thankfully, AD handles it well, IMO).
Some of this can be a bit off-putting depending on what headphones or speakers/subs you're coming from previously. As always, see if your thoughts change over time as you listen to them more.
Similarly, you can experiment with other front-damping materials along with or in place of the felt discs. I found a couple materials and configurations that reduced harmonic distortion in the bass without really changing the response much at all (verified with my measurement setup). You can try some various open-cell foam materials for this, which I have had good luck with. Believe it or not, a single-ply layer of tissue or toilet paper can also help tame the high end of headphones if placed in front of the driver. You might find this subjectively tightens up the bass. I actually have done so on my Mad Dog, so don't write it off as silly as it sounds. You could experiment with materials cut into discs or materials cut into squares to place directly in front of the driver, underneath other materials cut into discs.