Alright, I found a better unpacker and took a look, and if I'm not mistaken, I think I found the issue...
In the quarantine version's script_Locations.rpy, where the locations list is generated, I found the code (line 57) "Brotherhood" if "met" in newgirl["Mystique"].History and not IsGirlInParty():, which is followed by $ renpy.pop_call() and then jump Brotherhood_Entry .
These lines of code are missing from 0.984h_1 version (Also, in my few attempts to transfer saves between versions, I was unsuccessful). As an extra note, the file in the non-quarantine version is actually 7 lines shorter than the quarantine version, so there may be a number of other things missing from this and other files as well *shrug*
That said, I've not yet looked into repacking these files, and even if I did, it would take an age to upload at my speed, so someone else will have to fix and reupload.