Yes, there is a USB gadget of some sort loaded on the Kobo. All it seems to be doing is presenting the data partition to the PC. I suppose it must be virtualizing the partition table or something because the PC just sees the one partition.
As to the problem, if it is only the one Win8 machine, then maybe it is remembering something. Something I have done in the past to solve some connection problems for my Kobo ereaders is use USBDeview to delete the device. On the next connection, the device was reinstalled and everything was OK.
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