leo72:
Now the curious thing is that both of those systems use the relatively new Kernel 3.0.
If I try to use the Arduino as an ISP programmer from the terminal with avrdude, i strangely get that the sketch is written on the Arduino itself and not to the destination micro!
This sounds like a very big clue.
It seems to indicate an issue with AutoReset.
How are you disabling the autoreset on your UNO?
I'm wondering if the USB timing or virtual comm port timing
on the new kernel is such that it is now somehow causing auto reset to fail?
There are many things in the IDE and hardware related to autoreset and disabling autoreset
that are all working to together that kind of just barely work.
It would be very interesting to see a scope picture of the reset line on AVR in the
UNO being used for the ISP.
I bet it looks different in the cases where it is not working.
--- bill