This is exactly what happened to me. I was using a Sandisk Cruiser Facet 16Gb.
My box arrived with OpenATV installed. I played around with it got bored and installed the Wooshman image, got bored again and installed the ViX image, got bored then found that I couldn't used that USB stick again!
I've been having to flash the box on the fly. Even after returning to the Wooshman image I'm still finding that the box won't read the USB stick
I dug out an old 8Gb mSD card and USB adapter and that's working fine. :)