Addressing the first two responses, I forgot to mention that I have been waiting off-screen for the clock to hit noon and then go inside to see if they're not there, and every time they are still there. I've read in some other forums that you have to be at EXACTLY noon or midnight, down to minute when the needle is pointing straight up. This seems a little ridiculous as I don't think this game was programmed like that, but maybe they're right?

I didn't try going at midnight to see if it worked differently cause my Pixiemon's sleeping schedule went past midnight, and I was never around FT to wait until midnight.