I'm having the same issue.

Ubuntu Gnome 17.04 64-bits
Intel HD Graphics 530 (Intel Core i7-6700HQ) i965-va-driver
GeForce GTX 960M - NVIDIA binary driver - version 381.22

And I can confirm that this happens only when taking a screenshot of a
specific window. Either via the gnome-screenshot GUI or the keyboard
shortcuts.

Entire window or rectangular selection work just fine.

Also, this didn't happen with Ubuntu Gnome 16.10. I recently did a do-
release-upgrade and then started to notice the issue.

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https://bugs.launchpad.net/bugs/1672716

Title:
  Inverted colors on screenshots

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