Mine went in for the same as your's RobGTI and Steve30's on Tuesday - it had the APR trial remap (although it had expired and set itself back to stock) - BUT they said that they checked it on VAGCOM and no reported issues. So, they obviously didn't see the APR map, or they weren't alarmed about it.
Came out fixed - no chirping - hurray (only had 2,000 miles left on warranty

)
Personally I'd put it in, locked on the Stock setting, and see, but you takes your chances I suppose if you get a sh1tty dealer.