Programs Freezing When "Save As" Windows Appears

John's right that we need to more thoroughly check for spyware which can be as pernicious as malware. So in addition to the full SAS scan he prescribed, check each of your browsers Options for Add-Ons to disable all but FlashPlayer. Update Flash if you're ever prompted - check now if it's up to date.

Check brower Search that only Google is allowed in the stable search box which doesn't allow spying unless it's Chrome which is itself spyware. Tick the box to disallow anything from changing Google.

SAS goes even deeper to root any spying intruders out of registry where they sometimes continue to run if only uninstalled. But I'd tame it a bit by in it's Preference turning it off at Startup and disallowing updating except manually when you run it as a stand-alone scanner.

Just something to add, I've noticed now that when saving files on photoshop the folder icons aren't appearing but I can still save things. When uploading things to YouTube I go to find the file to upload and I have to fidget around with it a bit before if will work and even then the folder icons don't show up. Does this mean it's a problem with Windows Explorer?

See if you can restore the Folder Icon on the Properties tab of one of them.

If so then this might help: Default File Type Associations - Restore

What did SAS scan find?

Check your browsers' Tools>Add-ons that only Flash player is allowed, search is set to google only with others prohibited.

I wasn't saying that the folder icons not showing was that big of a problem for me. I was wondering if that could show if it was a problem that could be fixed by doing something like reinstalling Windows Explorer... if that's even possible...

Did a DSKCHK then SFC Scan. Problem still there.

Ran SAS. Found like 600 cookies and deleted them, problem still there.

Any other suggestions?

In addition work through the general Troubleshooting Steps for Windows 7 to go over your install thoroughly.

I'd include the hardware tests.