brent it's really weird - permissions look fine. They used to work perfectly before (I'm not sure how long before but maybe a few months), they seem to effect older Desktop folders more and, here's the kicker, folders where I recently compiled stuff.
As I was typing this I tested something - it seems to only affect folders on the desktop. I assumed it was the contents of a specific folder (it still might be, but its relegated to the desktop folder) doesn't matter if I didn't open them through the desktop, copying the same folder to the user directory and opening it from there seems to work out fine.