You create another Data folder? But doesnt that alter the path that is needed? Or do you copy everything in the original Data folder and in your folder? And when you pack, you pick the files from your Data folder or the Skyrin data folder?
I created another data folder elsewhere on my computer (Where I store all my modding extras), I then 'simulate' the data folder for just my mod's content in that alternate data folder. So I have something like C:/Alex'sCrazyFolder/Awesomeness/ModdingStuff/Madness/Data/Falskaar.esm Well, not exactly like that, but you get the idea.

Then I run archive.exe, and since the root directory is data, it doesn't have a clue what's above that Data folder. Then I just archive everything in it real fast by dragging/dropping the lowest level of each folder, I check the right boxes and click archive. Since my mod's structure within the real data folder, and my fake one is the same, the game loads it all properly and the BSA works. And I don't have to dig around Skyrim's/OtherMod's stuff to get the archive going.
@Alexander, I've added the solution to the wiki, hope you don't mind:
http://www.creationkit.com/Bug_list#Version_1.6.89.0
Of course I don't mind! I do think we need a page specifically discussing the fix, though I haven't the time to get one set up...
