My current project built with Sitecore 8 update 3 is well in to the build phase and I was starting to look at how components are performing and adding caching where applicable.
So I checked the stats.aspx admin page to make sure controls configured to be cached were being servered from the cache, [yourhostname]/sitecore/admin/stats.aspx , but my custom defined MVC site was not showing meaning I could not see the statistics for the sites controls.
Then I checked cache.aspx, [yourhostname]/sitecore/admin/cache.aspx, to see if my caches for the sites were being created and they were.
So I opened the Sitecore debugger [yourhostname]?sc_debug=1&sc_prof=1&sc_trace=1&sc_ri=1 to have a look whether my control was being cached and it was.
At this point I got in touch with Sitecore support to see if they knew what this issue was and as usual they delivered a fix.
After installing the fix I can see my custom mvc site on the stats page and the statistics for my controls.
If you are having the same problem get in touch with support and ask for Sitecore.Support.398176.dll and the associated config file.