Delete your trainer and re-download the latest. Then right click and run the trainer as administrator. See if that fixes it.
same thing with me. everything except the xp multiplier seems to work
I start a new game, activate this option, set the multiplier to 99 run into town and hit an innocent. Lots of skills leveled up. It works fine on my end. Maybe try increasing the multiplier to a high value like 9999 ?