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In addition, it isn't just the "JomSocial Front Page" that removes users ACL. (I have not tested all of the JomSocial links...but), so far it appears clicking on "JomSocial Front Page, JomSocial Friend Requests, JomSocial Friend Search, JomSocial Media (different links within), and certain profile links also cause ACL to be removed.
After some additional testing, the ACL rights removal isn't just happening when users click on the JomSocial FrontPage. It does appear that different pages within JS cause the same issue (tested on Friends, Friend Requests and a few other JS pages). The issue however is only when viewing JomSocial pages. Other components such as the calendar itself, project management, document downloads, contact pages and everything else within the site, ACL works normal.
This is weird, we cant replicate this on my local.. I am not sure this is caused by 3rd party or not.
But I think you should try to install the new Jomsocial installation on dev site, and test this issue again, and please dont install another extenstion only core Jomsocial and Joomla.
I've gone ahead and outsourced this problem to a 3rd party developer. Once they identify where the problem is at and fix it, I will post an update here in case anyone else runs into this problem.