Check For Malware Outside Of Norm?

First off Im running Avast and comodo and full malware bytes. But what Im wondering is if there is a way to check deeper for malware or issues? Reason Im asking is I think I may have downloaded an iffy program. My mouse seems to be studdering a bit ( and it didnt do it until now ) Im running a new build of only 1-2 mths old. So is there anything to look for in terms of processes etc? Or would Comodo, Avast and or Malware bytes have said something to me? Comodo kept popping up when I was installing it, but it does that anyway with any program.