as masterwork is a mechanic of it's own aside from mundane or magical crafting. then the price is actually 300 gp per 20 arrows(the amount that come in the equipment table). so while you can make up to 50 of them magical with the cost of making one sword magical. the masterwork part is made using the normal mundane weapon cost which is per 20 arrows.
so masterwork part would be 750 gp for 50 arrows (if your gm allow you to partly make only 10 of them) or 900 and your left with 10 masterwork arrows not enchanted.
50 Flaming arrows = cost of 50 arrows [2.5 gp] + masterwork  + Plus-1 Flaming  = 8752.5 gp.
Therefore 1 Flaming Arrow costs 175.05 gp.
Masterwork Weapons wrote:The masterwork quality adds 300 gp to the cost of a normal weapon (or 6 gp to the cost of a single unit of ammunition). Adding the masterwork quality to a double weapon costs twice the normal increase (+600 gp).
i stand corrected, 166.05 gp as Cevah wrote.(totally missed that part when i read it)