jazza

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
 

If you like you could upload three subs that cause the issue, along with your master flat/dark somewhere and I/we could have a look to see if we can reproduce the problem? 
I could at the very least align them by hand and 'blink' them to see if they show noticeable difference.
Just an idea. Bit of a strange one!