Official comment
Chances are your new computer has a different username or different iTunes library / path to the iTunes library, and as such, when you went to sync, it was effectively syncing a new source -- even if all the music therein was the same.
The way to remove them would be to sort by import date or location and toss all the newly imported duplicates, then re-assess your current configuration vs. your existing config to determine where the error was made.