I have to admit I am a bit confused over all of this speculation. My wife and I just took our first cruise in August and in all of the material I read, and all of my preparation, never did it come up about having your Rx in the bottles.
Like you I have the 90 day mail order bottles. I just went out and bought one the small "pill-a-day" holders and loaded up each day with the pills I needed. Between vitamins, alergies, and a few other Rx's, I had 7 pills per day. My wife had a container of her owns which had 2 or 3 per day. We placed them in our carry-on - which was only x-rayed at the terminal check-in at Philadelphia. It was probably sitting near the top of my bag - so it would have stood out pretty easily. If it was an issue - nobody said anything.
Maybe I was just lucky - but had no issues. The bad was not rechecked when we dismembarked in Philly. Perhaps if we had been checking out in Canada - maybe it would have been an issue - I really don't know.
I would suggest checking the State Department's website. If there are any regulations, it would be mentioned there.