So I am familiar with this issue and how to resolve (http://technet.microsoft.com/en-us/library/gg712698.aspx#BKMK_ReportBuilder3) and it was working before the upgrade.  I have upgraded two different systems now and the issue is back on both but the fix no longer works.  I have launched the console as admin and it made no difference.

Any ideas or things to try?  I saw a blog that indicated support for RB3 was in SP1 beta 1 but it most of got lost on the way to GA.

Yes, I know this is an old post, but Im trying to clean them up. Did you solve this problem, if so what was the solution?

Personally I launch RB outside of CM12 console. For that matter I dont recommend using RB, instead I recommend using BIDS, it has a bit more functionality.

Hey Garth - the solution (if I remember correctly) was solved after I upgraded to R2.  I haven't seen the issue since.

Garth - this fixes it

https://sccmentor.wordpress.com/2013/11/01/the-report-builder-click-once-application-does-not-exist-on-the-report-server/