I don't think I have heard of anything similar with a Kobo device. It is not happening here with any of mine.
What is the problem that Windows is reporting? My guess would be whatever that is is the real problem and causing the later crash. And if it isn't, then it needs to be eliminated as the cause. If the problem is that Windows wants to run a check on the disk, do it. It probably won't find any problems, but if it does, this might be the solution.
Other things to try or answer:
- Has it ever worked?
- Have you tried a different USB port or cable? Or another computer?
- Have you restarted the computer and device?
- Have you tried the Kobo desktop?
- What firmware version is on the Kobo?
- What version of calibre? 32bit or 64bit?
- Are you up to date with the Windows fixes?
- When does it crash? Straight away or after a bit of time? Can you see which of the connect jobs are running?
There is a fair chance that a factory reset on the device will be needed. If you do this, you lose the reading status for sideloaded books, and have to reload them. You can also copy all the files on the device when connected and restore them after the factory reset and checking things are working.