One thing that's possibly worth checking is the
internal power supply - that sounds like a lot of disks, and it's possible that if you're near your limit, then when your USB controller is working quite hard then it's overloading that limit.
You can see lots of strange things when near the power limits - I've seen graphics glitches, sound clipping etc.
This
checker will give you a value, though is quite hard to use. What rating (in watts) is your current power supply in the desktop?