Heyo Tommohawk,
Glad to hear you fixed it, just for completeness (please note I gave not an iota of consideration to background level or keeping colours nice etc, was just looking for the problem):
First off, no probs with your individual frames (do gifs work here? about to find out :D)
I just had a look myself and can reproduce your fun times if I try hard enough... so at least you're not crazy?
I can also however get it to stack just fine:
Method that works fine:
Load lights only
Check all
Register checked pictures (untick stack after registering)
Compute offsets
Load dark
Load Flat
Load offset/bias
Stack Checked pictures.
As you've figured out I suspect you may end up with too many stars if you dark subtract before registering.
Sorry for the large post