El Cap Slow to shut down, new clean install

I followed a Safe Boot suggestion by Linc Davis. I kind of suspected the usb ports. Because I just upgraded to ElCap and started getting sloooow shut downs. I added my profile at install. I did not have any of this with Mavericks. (skipped yosemite)

I did a completely new, clean install of ElCap 10.11.2. Haven't even installed all my apps.

I connected a usb hub. Actually usb hub was already connected, as I installed El Cap from a usb stick.

I tried not ejecting disk before shut down and ejecting disk. I tried disconnecting the hub. (the hub and stick are 3.) I dug out an old 2.0 hub and disk for testing. Still slow shut down. It's really less than one minute, but I am so used to just blink, blink, done...

So I tried your Safe boot test.

Booted in, had the usb hooked up and the disc inserted (both 3.0) and then shut down. Shut down was quick, no spinning gear (which is what I see when it's going slower).

Then I booted in normally. And shut down again. The first shut down was faster, with minimal gear time. Then did it second time and it was back to slower with spinning gear. It does shut down, it just takes time -- I'm guessing it's shutting something down.

This was not an issue with Mavericks. In fact, after one ElCap install, I restore my Mavericks from clone and booted up and shut down, all was normal. It only happens with ElCap. It's worse when I import my Mavericks profile. This clean install is an improvement versus that.

I've seen other posts about this usb / ElCap slow/hanging shut downs and startups. My startup is actually a tad faster with ElCap.

I tried removing all Log in items.

I created fresh (admin) user and tested, still slow shut down.

It seems like the more I used the computer, the slower the shut down was. But I didn't shut it down after every action I took. Like transferring files, setting up email, etc.

This is a 2011 MacMini. plenty hard drive (over 500 gb), max memory 16 gb, 2 ghz processor i7.

Have you any ideas? thanks