I just finished my mintyboost the other day and I've noticed that, after charging my phone for 10-15 minutes (I have an Epic 4G Touch being charged with 2 Eneloop AA's), the charger starts to cut out at irregular intervals for about a quarter second at a time. It's just long enough for my phone to beep as if it has been unplugged and plugged back in.
The batteries are freshly charged, so they are not dying. On the other hand, I have noticed that the LT1302 gets VERY hot when in use. It doesn't seem to be over the operating limit of 100 C but it is definitely too hot to touch.