Can you be a little more specific about which apps are not working? Or if you are using widgets or shortcuts with said apps? Maybe I can try and replicate and see if I have the same problem?
I put most of my larger apps on my sd card, sort of out of habit more than necessity... This phone has enough storage to run more apps than I could ever use but I've always had HTC phones with very little internal storage in the past, so it is just ingrained for me lol....