Hi townsbg,
Thank you for taking the time to have a look.
@ Bobby,
I do apologize for not responding sooner. It was not my intention to ignore you. I keep forgetting that once you get the first email notification that the thread has to be accessed manually to receive more notifications that someone has responded.
My specialty is the removal of malware and since RogueKiller is a tool used for the removal of malware, that is why I took on your thread and had you scan with other tools to determine if infection might have caused this corruption. The tools we used showed no since of infection, except for those undesirable programs that you had installed thinking they would resolve your problems.
Only thing I have not scanned your system with is a tool that would display if a rootkit is present or not. RogueKiller is able to detect and remove generic malwares and some advanced threats such as rootkits, rogues, worms, etc. though I took it upon myself to deem it unnecessary not to run another rootkit tool since you only mentioned in your first post that it detected PUP's (potentially undesirable programs) and PUM's (Potentially Unwanted Modification) detections which are not false positives or actual infections but rather settings which you may have made and in some cases, malware also makes. I saw no malware on your system that could cause this. Only programs that we deem undesirable because they optimize the system and can remove good files that lay idle and unused till they are called upon.
If you would like, I can have you run a tool that can will tell us if a rootkit is present, but I truly think what we have here is file corruption due to the use of optimizing programs.
Let me know what you would like to do. I'm still here.