It does sound like the bloke in the shop has wound the braind onto your reel incorrectly, resulting in twists being put into your braid. I know this as it was a problem I encountered when I first started using braid.
But you would think the bloke in the shop would know what he was doing!
Unfortunately the only way to fix the problem is to remove the twisted line and respool with fresh braid, only this time make sure you spool up the right way. I'm not exactly sure of the right way to spool a reel, I always get the bloke in the shop to do it, but i'm sure someone on here can advise you on how to do it.
Cheers
Gagga