As you might have noticed, our scouts were having some problems uploading bigger sketches. Occasionally (though sometimes almost every time), uploading would start, but then near the end of the upload it would fail with a timeout. This only happens on bigger sketches (>128kb it seems).
After thorough investigation (read this github issue for all details about this wondrous debugg-journey), Atmel has confirmed that this is apparently caused by a bug in the Atmega256rfr2 microcontroller we are using. They have suggested a workaround, but that requires modifying the bootloader, which isn't trivial to do (it isn't terribly hard to do either, if you have two scouts and we provide properly prepared code).
I still hope that we can learn more details about this problem and somehow devise an upload mechanism to work around the issue without modifying the bootloader, but it's doubtful if that is at all possible.
In any case, we're still working on resolving this issue