So I'd be tempted to agree mostly with Dr Styx from a design point of view. I don't think Paizo would increase the price of all the materials without putting it in the rules, leaving you to guess based on the cost of more expensive materials.
I was tempted to follow Dr Styx's formula, and obviously you have to pay double for the special raw material because its trade value is double its craft value. I was tempted, but then I found that Mithral has a trade price in Ultimate Equipment; 500gp/lb, so why would I suddenly consider it to be 360gp/lb (also, in the FAQ, it says you use the original weight of the item to determine price).
I'm going to use all the materials that have a normal trade value (Ultimate Equipment, page 93) and a special material trade value as examples.
Adamantine: normal price is 300gp/lb, easily-worked is 600gp/lb.
Cold Iron: normal price is 50gp/lb, easily-worked is 100gp/lb.
Darkwood: normal price is 10gp/lb, easily-worked is 20gp/lb.
Mithral: normal price is 500gp/lb, easily-worked is 800gp/lb.
Apart from mithral, these all follow a pattern; easily-worked material costs twice as much as the standard stuff (and the same craft value). This means that I can pay twice as much, and use the same craft cost to determine time (e.g. for easily-worked adamantine full-plate (market value 16500gp) I would pay (16500/4 * 2 = 8250gp), then complete 16500gp worth for crafting) and complete the item twice as quickly because it's easily worked.
This follows for flawless materials, as they have the same price. You pay twice as much for them, and the benefit (if you can call it that) is that the craft DC doesn't increase (does the base progress increase?) and you craft in the usual time.
This doesn't quite follow for malleable materials. I pay an extra quarter (375 is 1/4 more than 300) of the price and then craft towards.. 5/8 of the price? Which means it takes 5/8 the time to craft? This sounds wrong.
Same for pure materials, you pay an extra half (450gp/lb) and then work towards 3/4 of the normal craft cost, rolling twice, which again means you'll complete the item quicker.
In all cases, you pay more, and you complete the item quicker. It makes some sense, but it doesn't really seem balanced. In any case, I feel like the market value should be the same. After all, once completed, adamantine full-plate is adamantine full-plate. It has the same properties nomatter how it was made. If it was made to order, then you'd probably charge more for the extra materials to get it made faster.