I had the same problem with a VPN app that installed 50+ VPN configs. It seemed that the configs were registered but not the VPN profile such that the removal of the configs is virtually impossible.
I tried the followings with no success:
- overwrite the VPN configs
- reset Network Settings
- reset All Settings
- factory reset with backup restore (factory reset with no backup restore it does work but it was not a solution for me)
Finally, I found a simple (not elegant) solution to get rid of the VPN configs:
http://www.ibvpn.com/billing/knowledgebase/113/iOS-bug-fix.html
Enjoy!