I'll add a "me too" for this problem. Machine in question is a late-2012 MacMini attached to a CyberPower 825AVR UPS. Since upgrading to 10.11 (and then 10.11.1) Time Machine has been broken, only running via manual launch and when the machine is initially turned on. Following the procedures described here (disconnecting from the UPS) did not resolve the problem. Disabling Spotlight completely did not resolve the problem.
To throw another wrench in, since upgrading to 10.11.1, I've had the same problem with GoogleDrive- it won't load at startup, but will then launch manually; but randomly just "goes away".
I'm seriously considering backing out to Mavericks- it was slower, but the apps actually worked! I never paid attention to the console logs until recently, but the sheer volume of errors El Capitan is throwing is rather worrisome.