I'd encourage you to get the newer optiboot source from the 1.0 release candidate distributions...
When you say it only flashes after the initial ISP, are you saying you also see no flashes with a manual reset, or hard poweron?
I'll check out the 1.0 version, thanks - although I think I do currently have the latest, unless the Arduino 1.0 branch is a different version than 4.4.
Yeah, the problem was that optiboot (at least the version I have here), as noted above only waited for a firmware upload when an external reset was triggered, adding the check against PORF resolved that, allowing me to upload after a power-on (since the boards do not have a reset switch, although fashioning one is possible using the ISP pins, IIRC).
I can upload using the standard UART lines now after a power-on, which is a good start on my quest. I'll post another topic on the current troubles I'm having, which have little to do with optiboot, and more to do with my changes =)