I wanted to play GTA: San Andreas with my DualShock 3. Unfortunately you can't set the same button for 2 different things (like it is on the PS2). So I installed MotionInJoy and Xpadder, but Xpadder does not recognize any button at all. In MotionInJoy the Custom LED's and the Vibration test works fine, and this controller works perfect on my PS3. I am sure I clicked 'enable' in MotionInJoy.
Sounds like you haven't got the driver installed.
Check Game controllers in Windows Control panel see if the pad is recognized. In the MotioninJoy app go to the drivers page and install the driver with your pad plugged in.
I'd also recommend trying Better DS3 Instead of Xpadder.