oin

If you're having a MIDI track with a chain like this :
[MIDI In] --> [SquareGuitar] --> [Instrument]
Then if you record a clip, the recorded notes will effectively be different from the ones you heard, because it's the notes directly from the [MIDI In].

What you can do is having the SquareGuitar alone in its own MIDI track and change its MIDI output to the track you're recording to (or change the MIDI input of this track). I find this much more practical, since with this I can switch instruments and stay with the same controller.

Does it solve your problem, or was it something else ?

I discovered FRETpad recently and it totally changed my way of working with the Launchpad. For me, it's the most useful M4L device I've ever seen. That device rocks so much that I wanted to push the awesomeness even further and I eventually made my own version, with velocity/hold/modulation/pitchbend expression capabilities and the ability to switch to a standard guitar tuning, called SquareGuitar (http://www.maxforlive.com/library/device.php?id=1078). Even though I'm using my version now, FRETpad will always remain in my heart as THE way to free us, guitar players, from the supremacy of keyboards ;).