The reason why this happens is because the advert boxes are defined in the interface files or UIFILEs. When you patch Messenger with something like MessPatch or A-Patch, you actually modify that interface file to remove the block where the adverts are in.
A Plus! Live skin does just the same, only it doesn't replace the interface file in the Messenger executable file itself but in the memory space where Messenger is loaded, that's why you can switch between Plus! skins so easily! It doesn't matter whether the original interface file was modified before, Plus! simply replaces it with the skin's interface file.
What you can do is quite simple:
- Contact the skin author and ask him if it's possible to add some kind of ad removal.
- Modify the UIFILEs of the skin yourself.