Any ideas of how this happened?

Yes. If it's the bug I think it is, here's how it worked:

If you used Emplode 2.0 beta 11 and created a list of Favorite Visuals, there was a bug. Each time you synched more than once in the same Emplode session, Emplode would append instead of replace the list of favorite visuals. So if you made a change, hit Sync, then made another change, and hit Sync again, then it would instantly double the size of your favorite visuals list. There are some limitations to how the player can use config.ini, so once config.ini gets too big, things go wonky. And as you know, the way exponential numbers work, it doesn't take too many of these double-syncs to reach that point.

I didn't think to check this until you started talking about auto-switching visuals. Sorry we didn't think to check it earlier.

Please check to make sure you've updated your Emplode version (not the player... emplode) to the latest version, which has this bug fixed.