Why is it that wondrous items, armor, weapons, rings, rods and staves cost half as much as their market price to make, but the market price and the cost to make of potions, scrolls and wands are the same? Or have I been missing something the whole time I've been playing and D/GMing? Is there some place in the rulebook I've overlooked that says 'market price of wands, potions and scrolls is twice the cost listed'? Everything I've seen listed just says 50gp for 1st-level potions, for example, and that's the price I've always used for their price and cost.
You need to read the section on the feats for Brew Potion and the like. They also cost 50% of the market price to make.
All items other then potions, wands, and scrolls are discrete unique items that have a price listed and a cost.
Potions, wands, and scrolls are a group of items and they set the base price to purchase them in a chart based upon broad groups. The cost to make them uses materials equal to the 50% of the base price. See the snip below from the PRD.
To brew a potion, you must use up raw materials costing one half this base price. See the magic item creation rules in Magic Items for more information.
Well no wonder things always seemed off.