[kjetijor]

If I were to make a guess, you might be able to shave off some of the time it takes by enabling write-caching for the usb-device.

I believe that by default, windows disables write-caching for USB devices. Somewhere in the device manager, there should be a choice between "optimize for performance" (enable write caching) or "optimize for safe removal" (disable write caching).

[barrkel]

This would be my guess too. By default, Windows optimizes removable devices for filesystem consistency. For copying (or worse, moving) lots of files, that means updating filesystem metadata after every file moved, and flushing buffers. That kind of sync-interspersed random access will kill performance on hardware set up for sequential writes.