Two more things to check:
In
Edit > Preferences > MIDI - Playback and Recording make sure controller messages are checked.
Make sure the A-Pro is set to local control off.
But it kind of sounds like multiple settings or components are not quite right. Midi cable good? And when you say "standalone programs" do you mean playing just on your keyboard or do you mean using different software on your PC, such as a standalone VST host?