Sorry, user error. My "Include Files" was set to *1]*.* from a previous search where I was looking for duplicate .mp3 files and I didn't notice. That caused the access denied errors on some paths (I'm terrible with regular expressions so maybe someone can explain how that caused the problem?). If I change "Include Files" to *.* then it works fine. I've attached a full screen shot of my problem (I was trying to avoid showing my full name before), it does appear that many of the directories with the error were "linked" ones.
