pgas - thanks for the tip on the compiler (I think I have been trying various 3.x versions, but haven't gone back that far)
Because the SL6000 is a PXA255 (not PX270 as many others), I think this is why the RTC alarm wakeup problems. I have some thoughts on where to put a similar patch, so hopefully I can get a kernel to compile to test it...
plcg and desertrat seem to be getting the same behaviour as I am - everything works except the actual hardware wakeup!