I'm going to oversimplify in order to put this into terms that you can understand.
When attempting to clean up after a malicious piece of software (virus), there are at least two things that can go wrong:
Overkill, which means that not only do you completely eliminate the virus, but you eliminate significant parts of the functionality of your operating system that are required for normal system operation. So, while the virus is gone, your system is not working properly because whatever tools you used to get rid of the virus also got rid of essential system components or programs.
Underkill, which means that you think you killed the virus, but some part of it remains, or it did something to adaptively avoid detection (e.g. change its signature). If any traces of malicious code are still running, it may also manifest itself as similar symptoms to overkill; the virus may be operating in a reduced functionality mode for a while until you decide to go back to using your system normally, and then it re-manifests itself.
Since it is not generally possible to tell whether you've done overkill or underkill (the worse of the two possibilities is underkill since you may lose even more of your personal information to identity thefts if you continue to use the compromised computer), you should probably avoid the risk, and just reinstall.
Nuking the system from orbit at this time (including all except, perhaps, data files which have no executable components, like mp3s and images) would be highly recommended.