They weren't being installed to the same directory, right? Some games tell you to just unzip a patch into the base directory to upgrade, but DF doesn't, doing so will cause glitches. What's even trickier, sometimes you delete things from the DF directory and so naturally there'd be no conflicts, except sometimes there are STILL conflicts. Maybe DF has so much data that sometime we accidently place a new file before the old one is truly deleted (even though the OS says it is), and being that the data is rather compressed and non-redundant, just a few errors from this process make the new data noticably corrupt.
Best thing is to make a fresh directory for every instance of dwarf fortress, which essentially makes it a fresh, separate, clean install. Dwarf Fortress should leave your registry alone, it's really just an .exe that accesses various folders rather than an 'installed' game so it shouldn't get any deeper than that. Since a single save file is bigger than a fresh install of dwarf fortress, there isn't much of a downside to having multiple installs. I've never had a DF install go bad on its own, but when modding or switching saves or using utilities it's a good idea to keep backups and only have one active world per .exe.
Just to be on the safe side, if I wanted to do a lot in a given world (multiple forts, adventurers, etc), I'd make a new folder each time I started a new fort, and each time I abandoned a fort and started playing as an adventurer. That way, if something goes wrong, I can still go back to one of the older folders and the old save files are still there, unaffected.
The last time I had a broken install of DF that wouldn't boot, I'd recently been playing as an adventurer and had been making multiple backup saves. Sometimes I'd even go back to an older save because I decided to do something different at a critical juncture, and even though it appeared I cleanly deleted the saves before pasting every time, there must've actually been old (hidden) data that caused the data being copied over it to be corrupted.