The reason that a reset didn't fix it is because it will have changed the default font in the /system partition (which requires root). All a "factory reset" does is wipe /data and /cache, so it won't undo any changes you make to /system.
So you either need to try again with this app, find another font changing app, or make the change manually (since the phone is rooted this should be possible, it's just a matter of finding where the fonts are and understanding what you need to substitute - my phone is very low on power now so I can't poke around to see where the font path is). My advice would be to take a nandroid backup (a backup made using your custom recovery) before fiddling further with the system though, just in case anything else goes wrong.
The nuclear option, if nothing else works, is to reflash with a new set of official system software (which will remove root). Or if you are using a custom ROM, just reflash the ROM (no need to do a reset if it's the same ROM), which again overwrites the system partition.
