Mac Command / Control keys reversed.

I was running 2017.2 Intellij IDEA on Mac, and my editor tab crashed (while a process was creating a lot of files).

When I reopened it the Command and Control keys were reversed. 

So copy paste is now Ctr-C and Ctr-V instead of the Mac normal Cmd-C and Cmd-V.

This applies to all Cmd shortcuts, like save, refactor, etc.

When outside of IDEA, Cmd-C / Cmd-V work as expected, so it seems to be limited to this application.

I updated to 2017.2.5 in an attempt to remedy, no success. I am running MacOS Sierra 10.12.6