Ha! I've found it! (Maybe?) - with thanks to Wayne and DEcosse (in the charging systems diagnostics thread).
I think there must be a bad connection. Tonight, on a few starts, the voltage stayed in the low 12's no matter what RPM. A week ago, I got 14V and before that things checked out for the mechanic.
On top of that, just my luck, it seems like I've got yet another starting issue.
On Tuesday morning, battery fully charged, the starter wouldn't respond. No click or anything. Tonight I finally had time to go down and check things out. Fuses all ok... In frustration, I pulled the clutch in, tried, and repeated a couple times, just willing it to start. To my surprise after three or four tries it did.
It seems to behave the same every time, so I don't think it's dirty contacts (I started it four or five times). Maybe the switch isn't fully engaging? It would be weird if it was an ECU problem, since it happened even after the battery was disconnected and reconnected.
Somehow I don't think I can blame a failing switch in the clutch lever on the R/R issue.
Aside from all that, now to decide if I still go with the Ballistic or if I should just get a new glass mat. The parts guy is willing to change the Ballistic order to 12 cell. The mechanic doesn't trust LiFe yet and thinks I should stick with glass mat. Unfortunately, I pre-emptively bought a Clearwater Lights voltage sentry -- the LiFe version. Maybe silly, but part of me would rather pay more for the battery and use that voltage sentry than go through the hassle of selling or exchanging it.