Thanks for your reply, I can safely say I haven’t changed the subdivision at all, I done a quick test, I created my mask, polygrouped it, then I saved the file and opened it up again. Once i open up the file the same issue occurs, the polygroups rearrange themselves.
I found a solution however, or more of a workaround I should say, it was quite simple…
I deleted the lower subdivisions, and voila.
What I’d noticed before was that the issue only happened on a mesh with multiple subdivisions, the polygroup for whatever reason would rearrange itself based on the lowest subdivision level, so by deleting all lower sub’s I forced the mask to stay on the polys that I had assigned a group.
Hopefully this helps someone else who may have experienced this, maybe it’s a bug of some sort, who knows.