Try the latest test release 4.7.6. You can now set train departure times to the minute.
Car wait counts are decremented every time a train that can pull the car is built. It is not restored if you then reset the train. There's isn't an easy way today to understand that a car that isn't part of the train being reset needs it's wait count restored. Resetting a train releases cars that were assigned to the train, but a car with a wait count isn't assigned to the train, so the train "reset" function doesn't know which car wait counts were touched during the build.
Also car move and track usage counts aren't restored when using a train reset. So things can and do change every time you reset and build a train.
If you need consistent train builds, you should use the backup / restore feature.
Dan