Thanks for the headsup on the point of how much to be returned.
In my eyes it was not really usefull to recalculate every currency into yen just to not use it at the end because everyone will be paid only what is left on the individual currency.
I think that nearly no Euro are there anymore was because MtGox had withdraw problems on Euro for weeks and months before. Which was one reason why the bitcoin price was so high there. So no euros on their bank accounts might be the problem of high rejection.
I don't think, that that is a reason for high rejection, there are also not enough btc in there. And with that argumentation more than 80% of the real balance should be rejected (and that's not the case like Dargo already stated). The rejection or acception is only based on your balance. If not everything from you was accepted, although it is shown at your balance statement, then you should dig deeper for the reasons.
Maybe it is converted to Yen to make sure everyone can paid out, even if there are no EUR left. It is converted to Yen and then calculated how much you get. And based on this exchange rate, you will get euros.
PS:
I don't know if I'm right, just guessing like you. But I'm sure, your assumption is not correct.