I don't think the problem was on the mac - the mac flirc app worked fine; it's the linux flirc app that didn't; and on the linux box that the first time i plugged it in, it oopsed.
After that reboot and initial test I unplugged it, plugged it back into the mac to program some additional buttons, and plugged it back into the linux box, it was fine.
As this is probably my stable configuration now, that's probably it. And yes, I settled on the Samsung TV profile in an early post on this thread, as it turned out it didn't interfere with the other samsung kit actually here, and it seems to be working a treat. All buttons received by flirc.
So even with the hiccups, of course, it's settled to a hopefully final configuration within um, two and a half hours, which is still a huge win compared to all the other remote/receivers i tried, which took a day or so of sustained effort for at best partial rewards.
Summary of issues:
that first plug-in into a linux box that's never seen it before. In this case running ubuntu precise 12.04 64-bit; but can't rule out the error was in mobo usb controller.
flirc linux programmer doesn't recognise the device when definitely operational on same machine. (and seeing all those commands and no window, tell me it does actually have a gui, doesn't it? Didn't I see somewhere it's a QT app?)