Ok I think I made some progress on troubleshooting this.
I created a VM in Parallels as a brand new install of 2.0.6.5 32 bit and installed all modules and updates that you can get with the basic, extended and unsupported repos did a reboot and everything was fine, just as I have always experienced. Then when I went to commercial and installed sysadmin (2.11.0.40) and did an immediate reboot fail2ban originally started during the boot up until it got to where it says Starting Asterisk. When it got to that point fail2ban shuts down OK, but fails to restart, shows offline and the service will not start even when tried manually after its fully booted.
If I remove and install via YUM it comes online and survives rebooting.
I than ran update-fixes and fail2ban broke again. Remove and install fail2ban and it works again, however it resets the jail.local so I had to go to the system admin page in the freepbx gui and hit the submit button for it to rewrite the file properly.
During update-source it again breaks, but after it's all finished I can remove and install fail2ban again and it works. I still had to refresh the jail.local through the system admin module, but it's all working properly from what I can tell.
One a side but somewhat related note, when I run update-fixes it keeps failing when it tries to download fopfix29.tgz from all servers it tries. I can verify that my internet connectivity is just fine