SGO6 is not intended to work with the mod chooser. (It has its own uninstall, when you want to switch back to where you were before you installed SGO6, then just uninstall it which will restore the files you had in place when you installed it, simple.) Chances are you have exceeded the maximum number of mod slots in the Mod Chooser.
Strat and I have been in discussions about how to standardise the next version of the Mod Switcher, as him trying to anticipate the structure of all possible mods is pretty much impossible if we do not establish some standards for the Mod Switcher and mods to adhere to (though dealing with older mods that will not be updated complcates this situation even further).
The Enhancement Pack 4.0, if that is what you are looking for, is broken. It forces an install of the the old OP+4 Hardcore on top of the Standard OP+4 which will break your OP install. Pestalence has not been around for some time to fix it by using the new version of Hardcore in the Enhancement pack:
http://www.dynaverse.net/forum/index.php/topic,163365237.0.htmlI reccomed installing only the mods and improvements you desire one by one.