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My basic 1.607 without any custom plugins had different behavior: Only PATH didn't change (unfortunately I didn't confirm it was set correctly in the shell, so may have been user error), the new variables I defined were correctly updated.
Could you test whether the same issue occurs in the following configurations:
There was a specific change in 1.600 related to slave caching, but it should clear slave environment after restarting.
As there are, and were, numerous issues with env-inject being weird, knowing whether it affects things either depending on or independent of Jenkins version would be very helpful.