I've been playing around with, and been having a fun time changing up things in Rebellion, as I always had in Entrenchment. For reference, I'm on Windows 7 Ultimate-64 bit. However, there's one issue I've run into Rebellion, notably one that I did not run into on Entrenchment, and that error is that Rebellion has consistently crashed at under 2 GB RAM being used up, throwing me a "Ran out of memory" error.
Going by Windows Task Manager's memory column, this consistently happens in the 1,600,000-1,700,000K zone. This strikes me as odd as Entrenchment runs in the 1,800,000-1,900,000K without issue (I haven't managed to make it go past there). As noted in the OP, this is admittedly all occurring on modded Sins, though I'm attempting to reproduce this on vanilla Rebellion.