I have this exact same problem! It is driving me nuts due to how different the sim looks after the transformation ends. I do play with mods and have every game pack, stuff pack, kit, expansion pack however it occurs even with the mods removed. I did notice that it doesn't seem to matter whether the forms are linked or not and that the appearance change affected their body too.
My test sim(from the Gallery) looks like she magically lost weight, changed her entire face and had a breast reduction. I try to use the sliders to try to fix the changes but I can't do so, the sliders just don't want to move as much as they should like they're stuck at a certain level. I don't currently have any pictures to share but once I remove the mods again I will be taking CAS pictures before and after the transformation to upload.
Okay so I tested again with mods removed and the sims appearance no longer drastically changes after their first transformation.
