I think I have it setup how you described.  I exited Reaper and went into the Amplitube standalone version.  My audio input and MIDI input appear set correctly.  When I step on pedal 1, I see the MIDI indicator in the lower right corner of Amp4 flash.  But when I rock Exp B I get nothing.  No flash.
Here's a couple screen shots of what I have going on.  Can you take a look?