Hiya Chad,
Try going into the settings for PC Tools and adding the programs you're having problems with to the Global Action List as Allowed and see if that fixes your issues.
I have used PC Tools Spyware Doctor for 2 years now and have not had any issues with it at all, in fact I would have to say it's so far been the best one I've ever used, and I've used a lot of them lol. Good luck on it, but just for the sake of saying so, I don't think that is causing your issues with your programs not working.
Also you can right click the icon on the system tray and shut it off. Try that and see if your programs work then. If so, then definitely try adding them to the Global Action List in PCT. If not, then you'll at least know it's not PCT that is causing your issues.