pretty sure this is happening and I'm still having trouble getting it to work.
I know this is an ancient thread, but I was stuck with the same problem and found a solution for it. I posted my fix over at the Line 6 forums (http://line6.com/community/thread/51863
), since I'm using my BOSS FS-5U with a Line 6 TonePort UX2, but I'll summarize some of it here as well, for the benefit of others who might still be struggling with it.
The basic idea is that Looper's Multi-Purpose Transport (MTB) button requires the pedal to be in momentary mode and to send an ON message (i.e. val = 127) followed immediately by an OFF message (i.e. val = 0). I've been using CC64 for this (as someone, somewhere, in some forum said TonePort requires it to be so), but that may not be a necessary requirement. The reason it needs an OFF to follow each ON is so it can distinguish between a single click and a click-and-hold (i.e. undo/redo, while looper is running, or clear buffer, when looper is stopped).
So, the tricky bit is how to map a pedal that sends two values (a 127 when it's pressed down and a zero when it's released) properly. And the trick to that is to enter MIDI map mode, press-and-hold the FS-5U, then exit MIDI map mode before releasing the pedal. This ensures that the first value (i.e. the down value) gets mapped. If you release the pedal before you exit MIDI map mode, Live will assume you're just giving the MTB a different value (i.e. 0) and will ignore the first one. That trick (though not specifically referring to Looper) is in the MIDI/Sync FAQ: http://www.ableton.com/pages/faq/midi_sync#faq_2_link
MIDI Monitor (http://www.snoize.com/MIDIMonitor/
) was a great help in figuring this out.
 Based on Live's reference manual, any MIDI value 64 or above should count as an ON and any below 64 should count as an OFF, but I haven't tested it and 127 vs 0 is easier to read in the settings.
 Having screwed around with this for days to finally get it working, I'm really done testing scenarios at the moment. If you have time on your hands, feel free.