I also had the same problem and it is only with 1 adult female. She would shower in a formal dress that I downloaded from RoseSims.
So I went in to my Mods folder and deleted it. I went back into my game and had her shower again, this time she was showering in a maxis dress!
I went into CAS where I had saved a copy of this sim, and added her to the game. Same problem. I had her "plan outfit" to see which one was causing the problem. I changed all her clothes to maxis originals then had her shower. Great! She showered nude like she is supposed to.
So back into CAS I went replacing all her clothes one by one with the CC clothes she was originally wearing. After each change I had her shower and each time she did it nude!
I then switched households to play the original sim. Did the very same thing in CAS, lo and behold she now showers nude also. I have no idea why this worked or what originally caused her to shower in clothes.
I can tell you she was a sim I downloaded from the exchange and modified in CAS. Maybe she came with some kind of bug. Unfortunately I don't remember which sim I started her from to test that one!
Hope this helps in someway. I'd be real interested to now what originally caused it.
Yet another adventure playing Sims 3
Her smile was like a rainbow after a sudden storm...