What are the downsides of running DBCC FREESYSTEMCACHE ('TokenAndPermUserStore') hourly?
From Comments:

This sounds like a prime candidate for a Microsoft Product Support engineer. - Max Vernon


We experienced the same issue and our final decision was to use DBCC FREESYSTEMCACHE (&amp;#39;TokenAndPermUserStore&amp;#39;) on a daily basis. We consider the solution as more  predictable and managed than trace flags using. Unfortunely, MS wasn't able to find and offer some better solution.  - Denis Rubashkin


This is an old bug, I have a hunch that latest SP/CU should fix it. If not, you may need to contact MS support. As for question I faced this issue a lot in SQL Server 2008 R2 version and selectively clearing cache did not cause any issue. - Shanky