While we wait for confirmation, just so everyone knows a little more about what we discovered:
* The issue was a conflict with Mootools, which is distributed with Joomla and used on almost all sites, though some templates do prevent Mootools from loading
* The issue only affected the newer version of Mootools, which is included in Joomla 1.6, 1.7, and 2.5
* We didn't get to test if it affect Joomla 1.5 sites with the Mootools Upgrade plugin (distributed with Joomla 1.5.23+)
* The issue was not directly related to JFBConnect at all.
Hope that helps explain some things. Joomla is the largest user of Mootools (that we know), which means that this issue affected Joomla sites heavily, but not exclusively.
Thanks,
Alex