Q: Multiple Displays have problems with El Capitan

Luis has been a rockstar helping on this.  I believe there was one more thing that helped me -- DisplayLink has offered an upgrade in their software online.  Since I used the DisplayLink connection from the USB to the TVs, once I upgraded, things seemed to work fine ever since.  I have three monitors hooked up to my Macbook Pro.  Hope this helps

I have a solution that is a variation on the theme. I have a late 2014 model mac mini with two 23" cinema displays. The older models with the DVI connectors. I have one plugged in to the thunderbolt port through an adapter and the other plugged in to the hdmi port through an adapter. It was all working with Yosemite but when I upgraded to El Capitan I was disappointed to discover that only one monitor would work. It did not matter which monitor or which port I plugged it into. After restart only one would fire up. I tried resetting the SMC and I tried the NVRAM to no avail. I tried the detect displays bit also failed. I tried the SMC reset exactly as described here with no luck. I called a local apple reseller's service department and the fellow suggested that when resetting the SMC, during the first power up with only one monitor plugged in I should hold down the control-option-shift keys and the power button, and leave them all pressed during startup. I got to the login screen before I let them go. I logged in, and then when the desktop came up I plugged my second monitor in. It fired up and I now have two monitors. I tried to google the key combination but couldn't find it. The fellow from the store said it was supposed to make the computer start up, and then after a bit shut down and startup again. He implied that it is the most thorough way to reset the SMC. I don't know if that is true, but it worked and I am happy.

I use a Mac Pro 2013, running El Capitan 10.11.5. I have 2 LG monitors (model: 27mb85z) and connect them using Apple brand thunderbolt cables.

I've been dealing with this issue for over a year now. Every morning, it takes me 5 minutes to turn my F'ing monitors on. Turn off, turn on, turn off, turn on. Randomly it starts working... until later in the day when they sleep again.

Using it with one monitor always works. It's when I have 2 monitors connected and turned on that one of them doesn't receive a signal until I power cycle it enough times to get it to recognize.

I've also used my friend's dell monitor (their high quality 27 inch led model), and I had the same issues. I believe it to be an issue with either OSX or the Mac Pro firmware.

I have no idea how to compel Apple to fix this. But it seems pretty absurd to have wasted so much money on such a crappy experience.

Note: I've reset my SMC dozens of times. It does absolutely nothing to solve this issue.

SMC reset is our only hope in getting the 2nd monitor to work. We've been doing this since we upgraded to El Capitan and it's freaking happening to more than 10 macs in our office including ours, the IT guys. At first we thought it was the new 24" samsung monitors we bought from our trusted reseller but the monitors worked individually. This needs to be fixed. We are administering more than 70 macs and this is preventing us in upgrading all of our macs to El Capitan! We haven't had this issue in Yosemite though.

You probably install the same software on all the macs you manage.

Odds are some of that software is involved in the problem. Or maybe it is specific to some mac models?

I have used many different monitors and projectors with my mac (rMBP 2014) using EC.

It has always been plug and play. Not only that; the mac correctly recognizes the way they are organized (e.g. when I connect the iMac at the office in target display my rMBP knows to use it as extended desktop, to the right of the rMBP screen, whereas several projectors in classrooms work in mirror mode, etc); it has never failed.

Same experience with several of my coworkers, and all the macs at home (wife and three grown up children).

I suggest you try on a clean install, smc reset, nvram reset and see how that goes.

Worked!!! How I wish I would have done your 15 seconds of uplugged power before I spent what seems hours on the phone with Apple and at the Genius Bar coming up empty... Thank you!

Not to discourage apple, because I think the NSA leaked exploit is what's to blame. That and Apple can't stop Kanye loving their iPhone. Sadly, we have work to do Apple, I don't care about Kanye's iPhone 7. My Cintiq has been glitching with the last two El Capitan releases. I almost sent it back, that is BAD MANAGEMENT. Tim Cook, let me take over. (Cintiq 24HD works by unplugging the monitor FROM the power supply – the power supply stays powered for a while so unplug the MONITOR from the POWER SUPPLY)

I found that upgrading cables and multi-plexing issues are having a problem with the latest stable code base.

For instance this problem started in 10.11.5 and persists in 10.11.6 but I also have a 4K Displayport cable in one end, and a cheapo-cable Rev. 1.1 Mini DisplayPort cable. Rev 1.2 Mini DisplayPort Cable is current. Use the same together and make sure they are backward compatible, kaptain out.

It seems this issue with the multiple screens is ongoing since 2011 or so. After much research about it, I think the best solution is what some users have shared in this post: switch off everything, wait 30 seconds, turn on mac, then plug second screen in.