This is what I've seen:
Right after the last patch, the one where they fixed the companions to FT no matter what, my new companion FT'd with me when I was testing her sandbox package. I kinda assumed it was because they had made it so that any NPC set to player teammate would FT unless set to waiting. Anyway, I added Waiting after putting her into her Sandbox package thinking it would fix that problem but never went back in to check that it would solve the problem. The FTing only happened once, I didn't go back to see if it would happen again, it was so bizarre, unusual, unlike anything I'd ever seen in FO3, etc. that I just assumed it was due to the patch, which might not be true. Anyway, I just went in to test it (I've been busy doing other things and hadn't bothered to check before assuming it was fixable either way) and she stayed put both in Wait (her Guard pkg) and Sandboxing when I FT'd.
Did your wait and sandbox packages ever work during FT?
Oh, and before that, another companion I've made has a working Wait package that I can FT around with and there have been no problems.