From reading this thread it seems that part of the repair cost is being calculated on the "base value" of the gear. You are wearing the Legacy gear which is some of the MOST expensive gear in the game. That is why your repair cost is so high. (I think...)
On the contrary, the cost was just ordinary. And no, this was not legacy gear from vendors, but Binds on Legacy Sand people gear. Value of those items is unknown to me, but I am guessing the shell is the issue here, or some bug related to it. It would be pretty stupid from Bioware to punish people with DG shells for an example.