I did some more testing on the HR logging.. if the HR is disabled gcc works perfectly (as always), if the HR is enabled there are random problems: sometimes the phone soft reset itself, sometimes the signal quality drops to 0, and the only fix is the soft reset and one time the gps stopped reading (no data from gps) and the only fix was the soft reset.
These problems don't happen everyday, more like once every couple of rides, and after at least 30 min from the beginning of the log.
I tried changing ROM, and/or radio on the phone, but everything is the same.
Maybe the phone wasn't build to keep the mic-in open for so long and something overflows?
Anyway you said you could try to automatically close and reopen the wave device every x minutes, I think it's worth a try...