I had the same problem on my HP ProBook 450 G3 with IntelĀ® HD Graphics
520 integrated card and AMD Radeon R7 M340. I saw blue blinking not only
in Skype but on VLC as well.

Looks like it is a bug in the overlay in open source intel graphics
driver or in its default settings. In case of VLC, as workaround, you
can switch overlays off, but there is no way to do it with Skype.

Finally I found solution here 
https://github.com/linuxenko/ubuntu-skylake-i915-video-fix
Technically this fix just adds an instruction file 20-intel.conf, that tells 
how does Skylake should work. So, just add this file and reboot.

After that my video works normally.

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https://bugs.launchpad.net/bugs/1078068

Title:
  Video blinking blue during incoming call

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