It's not resetting the flag, but I have been pretty lazy about posting 5.1 "updates" for all ~30 of my addons, and when I'm pushing releases from SVN for addons that have not previously been updated since Patch 5.1, it is not automatically setting the flag, so after I push, I have to to the addon page and manually edit it to set the flag. In the past, I believe pushing from SVN has always automatically set the compatibility flag for the latest WoW patch. I certainly don't remember having to manually edit dozens of pages to check a box when MoP came out.
