ray1408:
Hi Jack,thanks a lot for your help. The boards are from Sparkfun. And everything worked very well with the old bootloader. Everything - exept one thing: the watchdog timer library (wdt.h). Which finally led to the decission to get the newer optiboot on those boards. The IDE is 1.0.1. I will try to manually overide with avrdude in the meantime.
Glad to help, if it qualifies as help at this point 
Not sure what to think, I have a 5V Pro Mini that I think still has the original bootloader. I could try updating it to Optiboot, not sure if that would tell us a whole lot though.