I don't think it's worth to start all over because of that problem, I'm playing for the second time now and it's still there. It is a little annoying when you have to reequip the items, but the skill level comes back. In my case patch doesn't fix it, don't worry to much, unless all of your items have bonus skills, that might get really annoying.
P.S.: Does it happen every time you reload or just the first time as you're starting the game (as in my case)?

...Carry on, into the horizon, wielding courage, staff in hand, journey through the shadows and dreams and what lies beyond the guardian's keep...