Hello & Welcome to the Forum!
Sorry to hear about your problems with the S - Polar Express.
Are you oprating in conventional or using the Flyer Chief Remote?
Check the switch located under the trailing truck to see if it is in the correct position, see page 5 of attached PDF.
If that doesn't fix the problem, refer to pages 22 & 23 in attached PDF.
https://www.lionelsupport.com/media/servicedocuments/6996749632250AFPEFlyerChiefset.pdfI hope this is of some help....
Happy Rails!
dave