The bike shop won't necessarily figure it out. They might just assume you are where they expect you to be.
If you aren't hurting, hey, no problem!
If you are hurting, hey, that IS a problem.
MillieNZ, if you can I'd recommend going back to the LBS and telling them the trouble you're having. It could be caused by a poorly-fitted saddle, or by a multitude of other things. If they fit you to the bike, they should do adjustments as well.
"If Americans want to live the American Dream, they should go to Denmark." - Richard Wilkinson