Is your comp old? How full is hd? How much memory are you running?
If you've done a lot of writing, erasing and rewriting, I've noticed it just makes entire os get glitchy. Which i assume is due to intense internal disk fragmentation.
I would startup from os disk if you have and run disk utility. Use disk first aid to check disk permissions and verify hard drive (repair as needed when program prompts you)
This is how I got my machine running better. Let me know if it helps.