I've had this behavior, specifically when doing operations that modify the key stack (layer up, layer down, etc). I'll do a Windows+left and the windows key will get stuck. I'm not sure if that's what's happening to you, however I've definitely had similar issues.
In terms of erasing the eeprom, are you referring to doing a `dfu-programmer <args> erase`?? This should be performed every time you're reflashing the board. It likely wont let you reflash without clearing the memory first.
