This issue has happened twice now on 2 different worlds.
I've found the end portal, put the eyes of ender all around, the portal effect appears, I jump in, then I get teleported to a random location in the overworld, with a nether portal behind me.
Does the End Portal work differently in FTB? This issue is almost identical to the nether issue I had previously (allow nether setting was false in the config). I've looked for an allow end setting but can't find one.