My suspicion is that when this happens for you, the reason is probably because NCrunch wasn't able to access the .ncrunchsolution file for your solution. This file contains a property called AutoEnableOnStartup, which is set whenever you enable or disable NCrunch. Is it possible that you have this file locked somehow? Perhaps using a read-only flag?
If NCrunch is losing other settings too, there may be something more catastrophic going on (i.e. source control system nuking the config files). Let me know if you manage to find a clear pattern that causes the problem, and I'll try to help you analyse it.