Do you have Transmit Riffs or Transmit Both [Arps & Riffs] enabled? I am not at my gear, so I can't tell you what menu system its in--probably controllers or arps.
One of the Tips and Tricks related to recording arps might help if you wanted to record arps. I think its in the first set of FAQs in the Files section. I had it out yesterday, but don't think I posted it because its about recording arps, not riffs.
Hope this helps.
Another option would be to record the riffs into a DAW [midi recorder] and use e-loader to put them into your E-Mu.