From your initial post, it seems like you had no issues when you used Yosemite. When you "moved" from Yosemite, OS 10.10.5, did you just upgrade to OS 10.11 or OS 10.11.1? OS 10.11 was somewhat "flaky" from the start, and in fact OS 10.11.1 started beta testing near the beginning of August, which was about 7 to 8 weeks before OS 10.11 was released. OS 10.11.1 was released about a month later. Myself, after being on OS 10.10.5, I went directly to OS 10.11.1. Besides wanting to avoid any issues with OS 1011, I also needed to wait for an upgrade to one of my critical third party applications (a couple of others were also upgraded, which I downloaded previously). But, for both of my Macs, I made a bootable backup first (as I always do once a week), booted from the external backup, used Disk Utility there to Erase and Format the (internal) SSD (again, on both machines), did a clean installation of OS 10.11.1, used Migration Assistant to "migrate"/copy all non-Apple system stuff from the backup, and installed the upgrades I mentioned. Everything is running smoothly for me.
OS 10.11.2 is currently in beta testing, but I am not sure if it will fix your issues. Maybe someone else who has/had such issues can provide more assistance. Here are details on the 5th release of that beta (released today):
http://www.macnn.com/articles/15/11...tches.tweaks.performance.improvements.131468/