You've got me really confused. First you say it works, then it doesn't.
When you reply to what follows, just tell me exactly what is happening. Don't speculate, prognosticate or tell me what you want to do.
JUST the facts.
1) In U_CC, in the MIDI IN window, are the stomps sending CCs 111-115 and the other pedals sending PCs? In EVERY Bank EXCEPT 18, in which :
Pedal 6 = PC#90
Pedal 7 = PC#91
Pedal 8 = CC#110
Pedal 9 = CC#118
Pedal 10 = CC#119
If NO THEN you STILL don't have the sysex loaded. I'm pretty sure I asked this before, but what MIDI Controller (the thing between the FCB and the Computer) are you using? FULL DISCLOSURE PLEASE!
IF YES THEN
1) go back to Amplitube standalone. IIRC, you're on AT4? In MIDI>CONTROL CHANGE>GLOBAL you should be able to LEARN Stomp A Slot 1-5 BYPASS to CC#s 111-115 using the Lower Row Stomps. You've also stated that the Expression Pedals work, which means that AT is receiving MIDI, in which case, if you CAN"T LEARN the BYPASS settings, but the Expression pedals work, and you tested the Pedals in U_CC as described above, then space aliens are interfering with your life.
2) In U_CC, UPLOAD what's in the FCB to U_CC (the square with the UP ARROW), SAVE it with YOUR NAME and attach it to your reply so I can look at it.