You can be assured it has been test ran. I saw several while there a few weeks ago running and being put through the paces.
That being said, check the PGM/ Run switch to see if it got bumped when the engine was put in the box or when you removed it.
Re-assign the ID. Lionel will often reset these to work on them.
If you're inclined check under the hood for a board that could of came loose in shipping.