I think I may have a solution to your problem, although I'm not sure what the cause is. I've done a lot of historical battles for the Arthurian Total War mod for BI, and I've sometimes found what you describe: that no matter what you do in the editor only one side is ever playable.
The solution I use (which is not ideal) is go find the historical battle file itself (it should be in data\world\maps\battle\custom\YourBattleName\YourBattleName.txt) First of all, check that the faction you want is listed in the "playable" section at the top. Second, make sure that within that section the faction you want appears first. So for example, if it displays:
Code:
playable
parthia
greek_cities
change it to
Code:
playable
greek_cities
parthia
If it still doesn't work, try going through the battle and copy-and-pasting the unit and layout info so the one you want is first all the way through. You'll notice that there are different blocks of text for both the units in each faction, and then further down the coordinates of these units. Change these around so that the playable faction appears first, making sure to keep the spacing between the block of text.
Hope that helps,
Antagonist