..after updating my map and updating the data file version to match the map version, my carts are crazy fast.

How do I fix this?

This plugin does not affect workcart speed.

Updating the data file when the map is renamed is recommended and is not expected to cause any issues unless the tracks have moved. Worst case, the trigger positions will be a bit off if the tracks have moved, but that shouldn't cause any other strange behavior like this.