more problems post malware scan and defrag than before

ok so, the little hiccups my PC has been having have tued into a full on dry heave. the issues i used to have were as follows: I have windows 7 and for some reason it keeps telling me to shut down to update, however it does not update most of the time and even when it does the little shield symbol remains. also it does not stay in sleep. it will stay asleep for a while but then the tower boots back up, thought it doesn't reactivate the screen. it will stay that was for a while before going back to sleep and the cycle continues like that. i don't think it's a mouse or keyboard as ive had the same one since before the new year and it only started happening this month

so hoping to solve one or more of these problems i ran a defrag ( the default one provided with the OS) and a malware/virus scan (malwarebytes anti-malware) and the result was now i have more problems

Now some (but not all) web players dont work, specifically ones native to tumblr and twitter, for some reason things like Vine and YouTube still function fine. i cant download any thing it just immediately fails. i cant open pictures using the default image viewer, it says i don't have the right permissions to view the file but alt image viewers work fine other programs are screwing up too, DivX Media Server says it registry is corrupted but the same error message keeps popping up again and again and when i just close the program it spazes out and i have to close it via the task manager. GeForce Experiance cant update and auto closes.

i have done nothing of note aside from getting a few game DLCs, downloading a new flash debug to play swf files, and adjusting the pathing in the registry so said flash play actually worked

i have no idea how this stuff happened did the defrag muck up my registry? did the scan delete important files? is my computer slowly disintegrating?

helping me solve ANY of the problems would be greatly appreciated