How are you assigning skills to quickslots? There are a couple of ways:
1) Keep the numerical key on your keyboard pressed for +- 2 seconds.
2) In pause mode, right click on the slot you want to quickmap.
3) In the skill screen, drag the skill icon to the quickslot.
Which of these options are you using and can you try the others?
Just to add my tuppence worth, I've always had problems with options 2 and 3: they work okay on an already assigned slot, but if a slot is empty it seems that only option 1 works successfully. I was never sure if it was a bug or just "one of those things"...
