My KDF one would transform properly, but in tactical mode my bridge officer tray would rearrange itself into that weird vertical arrangement we've seen on and off since the tribble testing of LoR and would go back to normal when it dropped back into science mode.
So it's definitely possible for it to transform properly but something about the whole thing seems to just be weird.
Got something similar with my Daeinos where it doesn't show it going back into regen mode. However, it has the abilities toggle just not the graphics, so for that ship it's purely a graphics issue. Have you checked that your Cmdr science ability comes back? It might be the same thing.
I seem to have the opposite problem, I get killed in tactical mode, I can't get back into tactical mode again. I just get trolled with a cooldown. Is that normal?
Criticism, while never agreeable, is necessary. It is like pain in the body. It brings attention to an unhealthy state of things---Winston Churchill
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So it's definitely possible for it to transform properly but something about the whole thing seems to just be weird.