Frankly, that shouldn't be possible (at least, given the information you've provided about the situation). Flashing the device doesn't just wipe settings, or reinstall certain things -- in imprecise terms, it just bulldozes over the entire root device, and gives you a completely clean install. The only cases that I know of where settings could persist would be if you restored a backup, or if you were running a cloned-to-SD install (Flashing only affects the onboard flash, so it wouldn't even touch an OS install on a memory card.)
As for your USB problem, I really don't have any idea. I suppose it's theoretically possible that other components in the device have small amounts of persistent storage for configuration or something, but that's complete speculation, and I would doubt it in this case.
Could you tell us what the nature of the problem is, exactly? That would help.