I updated serval of my Macs to 10.11.1 and began having problems. The mouse would get jerky, then freeze and unfreeze. I always display the seconds on the menu clock. They would stop for several seconds, restart and stop again. Eventually the Mac would freeze and stay frozen. So I rebuilt from a clean install of 10.11.1 (three times now) and it seems soon after adding TB2 8.8.5 the symptoms begin again. Just froze again so once I restarted I ran the TB2 Uninstaller. I'll see if the problem comes back.
However my feeling is TB2 is finally unusable.