Yes if it is a system32 error yes it can be bad. system32 is part of your boot files meaning the system files that order your boot (Computer Start-up) if these files become corrupt your computer will start booting slower and eventually not boot at all and if it won't boot you will loose everything. I would say if you still cannot find the trojan with norton make a back-up disc of everything you want and them re-formatt. A trojan is not a virus that stays in one place it will spread over a period of time.
