I got my 27" maxed-out iMac yesterday and after 9 hours of transferring data from my old iMac, the first thing I did is to update to 10.11.1. That's when many weird things started to happen: The startup progress bar started several times. Eventually it got stuck at 2/3 of the way and the screen went blank. I called AppleCare and they suggested I reinstall El Capitan. I installed 10.11 and that seemed to go well, but when I updated to 10.11.1 things went to bizzarroland once again. After several progress bar attempts it actually booted up and gave me a login screen. But I noticed that the Application directory was empty. All it had was a Utilities folder and that too was empty. While on the 3rd call to AppleCare suddenly files began to appear in the Application folder. But when I clicked on Google Chrome it beach-balled for some time and then said there was something wrong with the executable. They said try booting in Safe Mode. It came up, but again the Applications folder was empty. I was able bring up System Preferences (by clicking on the network icon on the title bar). But couldn't set anything: They connected me to the next level support specialist and she said I could swap out the hardware or get a refund since the Mac is less than a day old. But it doesn't look like a hardware issue. Perhaps some problem with the Fusion drive configuration? Anyway, have you updated to 10.11.1 on your new iMac and is everything OK?