One of the possibilities is that the output buffer on your player is not large enough.
I had something similar happening and increasing the buffer size has fixed it.
I tried tweaking the buffer in foobar, I had it up to 2000 range but it still didn't help.
Should I try setting it higher than that?
Thanks for the suggestion. I'll try and let you know how it goes
2000 ms is way too much. It should work fine below 500 ms.
If you're using WASAPI, then there's another buffer control in Preferences->Advanced->Playback->WASAPI. Have a look as my default settings were ridiculously low and increasing them to 250 / 500 (event / push) has fixed the issue.
The comments regarding drivers being up to date are valid too.
Adifer: I have the same issue with my HD598 E7/E9 combo. I'm waiting for Fiio to acknowledge this issue and resolve it. I am in an email conversation with them at this very time. Don't know if its a faulty unit or what. Drives me freaki'n CRAZY!!!! Tried all combinations and permutations of equipment, music, etc.. I have isolated the E7 as the issue. E9 works fine from my Envy 24 but I feel the E7 should sound better and work with the E9 as advertised.
SOLUTION (at least for me):
Not sure if this will help anyone else, but I have the same clicking and popping issue with my E17 when I use it with my notebook running Windows 7. It would start popping and clicking after a few minutes, the screen would flip between "USB" and the "lock" message and eventually the E17 would stop outputting music all together. Unplugging and plugging the E17 back in seems to reset the issue, but the popping would eventually come back. Changing USB ports made no difference (all the USB ports on my laptop connect to the same hub internally, that is shared with my mouse and built-in bluetooth adapter).
Curiously it only occurred if I am driving my Q701's and not my Reference X10's.
So, I thought it might be power related. I tried disabling the power management of the USB per other posts but that did nothing to resolve the issue. What I finally did was disable USB charging on the E17, and I have been running for the last hour pop-free! My guess is that my crappy work laptop is not providing enough power to charge and drive my "bigger" headphones at the same time. YAY!!!
Coincidentally, you should set your E17 to 24/96 all the time and see how it goes. In the Windows 7, Control Panel > Sound > Playback (tab) > select E17 properties > Advanced (tab) > Default format. Also check off all the boxes in the "Supported Formats" tab. You will need to unplug and re-plug the E17 for it to detect the changes (you should see "96K 24bit" in the OLED display)
I know some years have passed but there were no significant solutions for this issue. I experienced the same problem with the Fiio E18 as well as with a similar USB DAC unit from Creative. The Fiio works without any noise on my Samsung Android, but had significant pops and clicks (really loud too) on my Windows desktop. I changed USB cables and the positioning of the unit from the floor to my table (which is grounded). That didn't work. I changed the USB port from the front of the computer to a powered USB hub and that worked. I haven't tested whether this issue is related to the voltage of the USB port or if it is a USB 2 v. USB 3 issue. All those I assume are possibilities.