Thanks again Ayumi
To test this, I took one of the "problematic imported" blocks (who caused a duplicate plane warning) and deleted the rest of the map in a backup.
Then I only placed the "bad" block, and copypasted until I had 6000 blocks - gazillions of "duplicate plane warnings" but the map compiled.
So, since the compiler did not crash because of this, I think I can rule the "duplicate planes"-warning out.
Will keep on testing, this is all so strange