I got this resolved through help on Bugzilla. Here is a snippet of my final post there (thanks for putting me on the right track djc).
It looks like we can chalk it up to User Error/Bad Test Cases (of course). If there is anyone to blame (besides myself) it could be TortoiseHg. My test cases consisted of stripping commits and from one of the two repositories and then changing the phase of that commit in the other repository and push/pull again. It seems like TortoiseHg would pull in the wrong phase sometimes (possibly a caching issue). I can still reproduce this when I switch my server back and forth between publishing and non-publishing (but not quite as consistently before).
However, doing a command line pull seems to get it working every time. I was using command line to check outgoing/incoming, do the phase changes and such, but possibly never used it for the actual pull.
Sorry to waste everybody's time. I resolved it as invalid, not sure if someone wants to change it to a better category. Let me know if there is anything else you want me to check or expand upon.
I'll edit in any updates, let me know if anyone is still having trouble with this.