Ok, cheers!
I just did a bit more testing and think I figured it out. If you have file names without velocity layers (e.g. "ShortBass_C2.wav"), the tool will fail if you leave the velocity detection pattern empty. It gives the error:
"Could not create multisample: Could not detect MIDI note in file name: ShortBass_C.wav".
Adding in any old velocity detection pattern (e.g. "v*") seems to work - you obviously don't end up with any velocity layers, but it does allow the tool to run without any errors.