So I looked in to this issue and found the cause:
When you load a character SWF file it can contain a chunk of code to change settings automatically.
In certain files, you have the parameter "skin", which of course changes her skin tone.
When this parameter is parsed, the function "setSkin" is called.
Within this function there is code that targets mod elements and removes them, resulting in that effect.
Now that shouldn't be happening. Surely Kona would load the code first, then apply elements right?
And that he does, it's a really unique problem here.
The loader is too fast.
What I'll do to sort this is push official mods on to a list and have SDT parse them itself, that should make vanilla mods solid.
EDIT:
It's fixed, but the solution is disgraceful.
I load all mods, loader or otherwise in to SDT. Basically throwing them all at it, and Kona's error handling makes sure only vanilla sticks.
After this I actually parse loader stuff independently. Nice batch loading function Kona, appreciate it.
Expect bugs.
If you're interested in why this works, allow me to explain:
In the same way I can monitor the loaded state of a loader SWF, Kona controls the state of vanilla SWFs. This information is (probably) unavailable to the loader so it just loads one after another without checking because it (probably) cannot.
Kona can monitor the state of the SWF and as such pace the loading properly.