When using the GenesisExtractor you will stumble upon daemons that simply won't work.
They will either crash or not follow standard procedure (like for example they might not accept external -datadir parameter to tell the coin where to save its blockdata).
Their daemon/tool might be very specific and not accept any of the usual commands you would expect, like getinfo, etc...

We need to get a better understanding of how many altcoins behave differently than all the rest, and why.

It would be helpful if you could post about non-standard coins in this thread (preferably also with screenshot).
This way you will help us improve the GenesisExtractor and also our coinID list.