Hmmm…If you haven’t already, try these:
Place a couple of the direct dial shortcuts on your home screen and try using them to make calls just to make sure they work from there
Rebooting
Uninstalling and reinstalling SwipePad, then programing the slots again with the direct dial shortcuts
Reboot into recovery and wipe cache
If you’re using a theme other than stock, go back to the stock theme and try it
Those are things I can think of for you to try. Also make sure you’re using the latest version of SwipePad from the market, 0.8.7. The previous version had an inability to add an app in Miui which has been fixed in the latest version – even though getting an app to open isn’t your situation. You could also try emailing the developer of SwipePad.