I'd suggest that its something to do with the mark up as you have it set at 60% of the value to sell at, (you'd be out of business very quickly that way) set it to 120% or preferably set the price manually gets rid of annoying fractions and GP/gp costs and you can decide how rare in cost certain items are.
For example using the Half plate +1 Armour from the item list cost 501-5,000 gp adding it to my shops inventory (set at 110%) gives a base price of 1052.01 gp, which I would manually change to 4,500 GP as I think it reflects the costs better.
hope this helps

