So I have been running a Piwik server at home for a while now and I just updated a while back, my website has had no major traffic increases.
Every page load on the administration panel takes around 15 seconds to load during which my CPU is at 100%, I have checked and my MySQL server is fine, It only uses about 20% then its out, it is Apache which is using all the resources for that 15 seconds.
I have made no changed to my PHP / Apache configuration but it seems to only do this after I updated.