Hello:
If I read your post correctly, it sounds like your problems only happen at start up. If so, consider a powered USB hub. The issue could be related with Windows scanning the USB ports at startup and assigning them in a different order from the previous boot up. So HW or your audio driver can't find them. You can search the forum and see previous posts regarding this subject. A powered hub reduces any ambiguity of connected USB devices with Windows.
I have Windows 7 and the last few weeks at boot up I consistently get the HW warning that it can't find my Roland UM-One USB MIDI interface. To clarify, the issue is not HW but Windows! So while my computer is booting up, I simply unplug and re-plug my Roland USB connector. Granted this is a 'band aide' approach but I avoid the HW warning 100% each time. My next step is to reload the Roland UM-ONE driver or swap in my spare iMio USB interface.
Danny B.