I think I've read every romance thread here and couldn't find an answer to my problem, any help is greatly appreciated.

I've installed the multiple romance script v2 and AerieRomanceActive just changed to a 2. The other two NPC's variables changed to a 3, which I assume is not supposed to happen.

I used Shadow Keeper to change the other two variables back to 1. Will this cause any problems?

I'm going to go out on a limb here and assume that you didn't do any of the following:

Kick other NPCs out of the party.
Be mean to other NPCs, ie. choose the wrong dialogue options.
Other NPCs didn't leave the party for a non-game related reason (ie. reputation beyond acceptable limits).

If none of those occurred, then there's a problem with the romance pack.

I don't think that setting the romance active variables back to '1' will kill anything, but they may just switch themselves back to '3'.

You are correct, none of those items took place. Everything was fine until this last dialog which put Aerie at 2 and the rest at 3. Editing the savegame with SK didn't fix the problem either. As soon as I load the game the other two NPCs switch back to 3.

I also tried reinstalling the mod. I'm going to see if setting the variable at the console helps and if not then I'm going to reinstall everything and make sure I have the patches/mods in the right order.

Thanks for the help.

No, I don't think the console will help anything, as the variables will just reset every time you load, forcing you to start all over again.

More than likely in is an "installing out of order" issue. Either that or the multiple romance mod is broken. Maybe you didn't install it early enough...who knows.