I appear to have found a bug on the Windows version. I accidentally turned off transitions and now it appears the transformations aren't working no mater if it is reselected or not.
Viewing post in Furry Chronicles - Bug Reports
Not fully sure that was the cause. I did that pretty early on, and hadn't actually run into Cola or Luna yet. Just my best guess, but Cola and Luna transformations aren't happening. It might just be a windows version bug, but if it was that option it's tied to the saves too because I reinstalled the game with no success in fixing it. Your companions seem unaffected regardless is it's checked.
Also congrats, you really got me on Luna the first play through, on the web version.