Oh crap, an "old" AMD system. (Says the guy still rocking socket 775.
) Well, at least it won't be
this problem then. And you've got the best onboard audio codec of its day, the ALC889... even ADC filter ripple is superbly low. [1]
Here is one guy who had issues with USB on his 990FX board, maybe one of the things that came up there would help. According to
this, the BIOS setting for IOMMU may be worth checking, as well as making sure the latest BIOS is installed in general.
Here's a guy with another 990FX board who says he's been fighting USB dropout issues "for years". And
here is perhaps the most interesting hint, a guy with a DAW who got dropouts as soon as he turned on AHCI (which is always on these days)... seems ASMedia SATA controllers are sus. You don't have one of those, but you do have an Etrontech USB 3.0 controller to complement the southbridge's 2.0 ports - which ones were you using?
I suggest you run
LatencyMon and have a look which drivers may be causing problems.
[1] Actually, you know what? If that works flawlessly for you, you could use some external gear to handle the conversion from and to balanced and levels and stuff, much like I am with an Asus Xonar D1:
I have a Mackie 402VLZ4 that goes into the line-in and can handle a pair of mics or guitars plus a pair of balanced line inputs plus another pair of unbalanced inputs. Master gain is set at about -9 dB so that input clipping (2 Vrms / +8 dBu) coincides with a healthy +17 dBu internal level on the mix bus (it could handle about +22 dBu); you would want to set this another 5-6 dB lower because your input can only handle ~1 Vrms.
I only have my monitors on the output so a Behringer HD400 plus assorted cabling (3.5 mm to 2x TS, 2x TRS to XLR) does the conversion to balanced sufficiently for the most part, and passively to boot. Those not averse to DIY and having a way to determine their output impedance may want to solder up some impedance-balanced adapter cables instead.
(You could get a mixer with an FX/AUX bus - like a Mackie Mix8 - so you can do a
mix-minus and thus listen to computer output on the mixer main/headphone out while recording sources, but that's only worth it if you're happy recording in mono only. The Aux Send on that one is impedance-balanced so you could run that into a stereo line-in as-is and subtract the channels in your audio editor / DAW for a sorta decent balanced connection, so there's that. The reason I'm suggesting a Mackie is because they have an overall Aux Send gain control in addition to input channel pots, which again would be better for level matching as discussed above, and like any decent manufacturer they provide a block diagram. The Behringer Xenyx 802 has a gain on the Return side only, which is useless in this case, and you have to figure out the signal flow all by yourself. Lots of noobs are using Behringer gear, so their poor documentation is a real minus in my book.)
This setup is not as low-distortion as a Scarlett 2i2 gen3 (which wasn't out yet when I put it together) nor are the drivers a source of joy, but I reckon it achieves somewhat better dynamic range than the gen2 with similar (maybe a hair better) microphone EIN, distortion not degrading even at highest mic input gain and tons of overall gain on tap if need be, and cost me substantially less. Converter wise, the ADC is almost the same and the DAC is better. You probably have to enjoy tinkering with stuff and being thrifty to prefer a setup like that over a "plug'n'play" one-box solution.
BTW, when using an older Realtek chip like that, avoid recording at 44.1 kHz like the plague. Use 48, preferably 96 kHz. I'll have to try
AAF modded drivers one of these days.