Couldn't remember how I had reconfigured capsule to play the whole track, but it was by substituting the inter variable with the whole track length:
track_length = len(track)
if verbose: print "Computing transitions..."
start = initialize(tracks[0], track_length, trans)
# Middle transitions. Should each contain 2 instructions: crossmatch, playback.
middle = []
[middle.extend(make_transition(t1, t2, track_length, trans))