OK, I figured something out: it's not the amount of the files, it's a memory leak.
The overall size of the files matters, not the amount. It can crash on a single file, too, if the file is bigger than 100MB or so. I checked in the task manager, during the conversion the memory size and the VM size constantly increase, and the memory size hovers around the same size as the write IO size -- meaning, that basically the process keeps in memory everything it writes into the file. When it reaches 100MB or so -- crash, access violation.
Maybe I should try earlier versions?