Hnnn. I tried once more, and it bugged out again at 20080201.gpf...
It looks like it finishes at 99%, goes to 'process patched files' and *then* bugs... the first time I followed loki's advice and wasn't watching the screen the whole time near the end, so it might well have bugged out at the 20080201, all I specifically remembered was that it was after the 20080125 file...
I tried uninstalling heRO and then reinstalling it, and patching again, but the heROpatcher bugged out once more.
The game itself seems to run fine aside from some messed up pallets and whatnot. Still, its rather vexing.