Hi Peter, I am a great believer in always looking at the last thing you did when something has gone wrong. I suspect what you have is clutch drag caused by the thicker new plates and no doubt some new oil. Its not unusual for the 250 motors to be hard to get into neutral and always seems to get worse if the motor is disturbed. With the bike on the stand the back wheel can spin so the clutch does not have much effect dragging or not.
You may just have to get used to slipping the bike into neutral before coming to a halt and if you forget then you will just have to hold the clutch in until you can pull away again.Since you state that the garage road tested the bike I am assuming that the clutch does actually work, its just an issue getting neutral.It will probably bed in over time ( but do make sure your clutch is adjusted properly)
Regards
Peter