Before moving the .pk3 files out of their install folder, you had to unzip them.
So, to be more specific
, try to :
- install the most recent v2.6 build you have (or, to make a quicker try, just move back the .pk3 you removed in their original folder).
- go to the folder where the game is installed.
- unzip all the .pk3 (i did it with 7-zip, "Extract here" option).
- move all the .pk3 to another folder (I moved them in a "New folder" that was not in the UFO:AI folder)
Please tell me if it works (it worked for me with the build of the 9th september, thus it should work with more recent builds).