One bug report later: 46784
It turns out that any that modifies data.raw["gui-style"].default in any way will appear in the disable list. My mod does that by creating a custom sub-style.

So basically any mod that creates a button style of its own even if it doesn't use any images appears in the list. Anyone know of a work around for this? The new 0.15 pre-defined button style(s) might work but I'd have to check them over first.
I was looking for all the ideas people might have. FactorioMaps being the mod I'm trying to "fix".