Sip registrations and settings not writen to sip_registrations.conf sip_general_additional.conf

I recently upgraded to version 2.6 from 2.5 through the online updates. Since then there are no registration strings in the sip_registrations.conf and astersik does not register to providers.

I deleted the database, installed freepbx again from scratch. Restored settings from backup. Again the same problem.

Digging a little deeper, any changes made in the web gui are reflected in the mysql asterisk database. However even after applying changes on the webpage through the orange bar, the new settings never make it to sip_registrations.conf or sip_general_additional.conf. Doing a sip reload on the asterisk console and then inspecting sip settings or sip registrations again show no changes made in the web gui to sip NAT settings, and no new registrations show up.

There are no problems accessing the asterisk database, I get no errors from freepbx, and as I mentioned, changes made are reflected in the mysql tables.

Interestingly changes to iax settings also never make it, but changes made to sip extensions do show up in sip_additional.conf and the new extensions will show up on the console on doing sip peers or users. New trunks also show up, however new register strings for the trunk never show up, sip_registrations remain blank, doing sip show registry does not show any register strings on the console.

I am at a loss here and any help to debug and sort the issue would be appreciated. I am running on Ubuntu Karmic, asterisk 2.6, the webserver is running as asterisk, all permissions on freepbx directories as well as asterisk files and directories are correct as asterisk:asterisk.The web GUI functions perfectly and gives no errors, but the changes made are never make it to asterisk. The same setup was working perfectly prior to this.