I think it's great that you finally got the game onto Steam, but someone needs to take a moment to put the Steam version through its paces.
So far I've noticed two things.
If you take a screenshot, the act of using the Steam overlay kicks you into decision mode. Or at least I think that's what happens, because all of the regions on the map turn pink. This is not the end of the world because the effect can be stopped easily enough, but people who use Steam products are accustomed to games on Steam having the same functionality as the non-Steam versions.
On a more serious note, if you call up a leader, none of their tabs (overview, combat, mobility, etc.) do anything when you click on them. People who don't have the non-Steam version won't be able to tell the difference, but if you have the other version it's easy enough to compare and see that something isn't right.
Please have your beta testers review a product before it gets pushed onto Steam. The Steam overlay does a whole host of weird things to games, and you can't just assume that everything will work in Steam the way it did in the non-Steam version.
[Note: the issues that I'm having seem to be entirely related to the Steam overlay. I turned the overlay off and the issues evaporated. While I don't recommend going on Steam with a game that isn't compatible with the overlay, if you are going to do that you need to put up a big sign in neon lights telling people what to turn off before they try to play the game].