Ok, I believe I have it figured out. I went back through all of the global settings and noticed that reappend non-sef variables was not turned on. I added it and this issue seems to be resolved. Now on to figuring out other community builder duplicate issues...

Thanks for the help.

since I posted this, I upgraded to the paid 3.6.1 version of JoomSEF but the issue still persists. Below is a screenshot of the settings for custom non-sef variables list:

I have a general question: How do I ensure that certain variables show up in the generated SEF URL? I am using alpha user points and some of the variables associated with that extension are not showing and therefore do not allow the user to see certain pages (ex. CID for medal winners lists).

Also, users can't see their referral id in Community builder. (ex /index.php?option=com_comprofiler&task=registers&Itemid=&referrer=AUPRS-4B4B42E44B5DF)

I've tried adding the variables names (cid an referrer) to the custom non-sef joomsef extension rules for these components but it doesn't seem to work.

I didn't see any documentation about using variables in either the documentation or FAQ area.

Please help!