Rockbox Ports are now being developed for various digital audio players!
You could try the retail firmware and see if its any faster.
Maybe formatting using these instructions will have better results than using Windows.
I haven't seen reports of Rockbox's USB mode causing problems since it was enabled and I haven't experienced problems, myself. Slower transfer speeds (compared to the OF) are to be expected, but this obviously doesn't explain your previous trouble. You are also seeing much lower transfer rates than you should get, even with the OF. Maybe some factor like a bad cable/port is giving flaky connection while you are trying to move data. Intermittent disconnection while mounted as a UMS device can lead to file system damage as well, which seems consistent with some of your previous symptoms.
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