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Eclipse import throwing java.lang.NullPointerException and fails subsequent validation.

I have a very large project that is ready to deploy. However, before deployment we want to move the project from Eclips on Mac OSX to a Windows system. Both systems are running the latest Spring '17 Force.com IDE and Eclipse Neon.2 Release (4.6.2).

The project passes validation when tested from the Mac, however when exported and imported on the Windows system, the import first throws a java.lang.NullPointerException with no furhter details and then fails validation. I have looked at all the contents, and they look to be identical.
Andrew EchevarriaAndrew Echevarria
You should check the compiler settings and make sure they are using the same JRE version
Compiler settings both look the same, using compliance level 1.8 etc. I tried reinstalling the JDK and Eclipse on the Windows system, but that had no effect on the problem.

And to reiterate, this problem does NOT happen with an export made prior to the Spring '17 update. Using the same JDK etc.