If you have a HID connection eg USBkey with the Atmel PC test app. the PC gets stressed when you interrupt the connection like when resetting the uC.
The PC processor load is increasing by 50%. It keeps on working. If you do this a second time the PC loads is 100%. The only way to stop this is to exit and restart the PC app. ( both W2000 and XP)
I have this problem also whith my own Delphi prog with a different HID driver. Nothing helps, even closing and reopening the HID component.
Funny thing USB: Made an application (MMC) what immediatly resets (CLICK!) my old W2000 PC, all other (W2000 and XP) PC's are working OK. It is not the hardware. Noticed that XP is far more tolerant on USB enumerations errors than W2000.