And I have a real big map , with many new regions added (but no new rebel factions)
Hello,

You do not really need to make new rebel Factions, even if you have new regions, you can use the pre-existing ones...

Now, there could be noumerous things that cause you to CDT.

But from the Info you have shared here, the one thing that comes to mind is..

descr_strat.txt

have you assigned the new regions to the Rebel Faction?

Look for

Code:
faction slave,
And make sure any new regions that you have not given to the other factions are under that.

Hope this helps