Apparently the rollers are lining up exactly with the dead areas on the switch.
If its feasable , you could try turning one or both of the tender pickup rollers 180 degrees and see if that makes a difference.
I know other members have done this in the past, possibly even with the first run S3
Another option is to run a hot wire from the loco pickup back to the tender pickup. This is obviously a bit more work/ modification.