Sounds like you did not give the second install a different database prefix. So, that merged the two sets of information. Since there is a little know law of physics that says no two objects can be in the same place at the same time, your gallery option for the zenphoto release was set to the one for the new installation.
Since {remember from a different thread} zenphoto always checks the built in release level against the level stored in the database and, if they differ, insists on running setup.php, you got setup run as it should.
If you just run setup, that will restore the release level to the one from your base gallery. If you uploaded any images/albums to the new gallery, they may have got loaded into the database. If there were no conflicts, a refresh database should clean things up. If there were conflicts, go for the backup.