On boot my Pi shows the standard Raspbian desktop, but then it switches to tty1 and I have to use Ctrl+Alt+F7 to get back to the desktop.
How do I fix this?
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I've experienced the same problem on 2 separate, new installs over several weeks. Xserver starts up with Pixel, but then I'm taken back to TTY1. I have to Ctrl-Alt-F7 to get back to it. To reproduce, take new install of Raspbian Jesse + Pixel, then do "sudo apt-cache update && sudo apt-get upgrade". Reboot.
Have you installed RetroPie by any chance? I've compiled and installed retropie from the git repo on both installs. It has its own boot options just like raspi-config, and I've considered that this behavior might be related.