Inactive extensions keep getting added back in as iSymphony users

I submitted a ticket with iSymphony, but was told that they don't think the issue is on their end.

The issue we cannot figure out is that the iSymphony Settings for all extensions somehow reset themselves to;
Add to iSymphony = Yes
Create User = Yes
Full User = Yes

It happened after installing module updates once (not sure if iSymphony module specifically), but then I think the last two times it has happened without an admin being logged in. We do not have System Admin installing automatic updates.

We do not want terminated employee extensions (extension needs to remain for some time), or conference rooms and the such showing up in iSymphony, so we have to go in and set those three options to = No for quite a few extensions each time it happens. 
Why do these three settings keep getting reset to Yes on their own, and how can we prevent it from happening in the future?

This never happened before upgrading to the current FreePBX Distro (13.0.192.19). We were previously on a very old version.