task manager locks up/program start up super slow

I've seemed to develop some kind of problem in the past few days and I'm not really sure what to do about it.

Some programs start unbelievably slow (up to 2 minutes). Programs range from Photoshop to notepad. I click on the shortcut (or exe) and it seems nothing happens, then about a minute later the pc starts making the working noise and eventually starts the program. Some programs start just fine, firefox and all my games start up just like they always have. Games run fine and cpu usage is low.

Also, if I try to kill a process from task manager it seems like the computer locks up and several minutes later the process dies (during this time the pc sounds like its working hard).

I've recently has a malware problem but have gone through all the steps in the malware forums and have gotten rid of that as far as anyone can tell. I also recently turned off a bunch of windows services but have since re-enabled them when this problem developed. I may accidentally turned something off that led to this but as far as I can tell I’ve turned all the default services back to their default settings.

Any ideas? Thanks