I am also facing the same issue, I have tested this with the bank account payment method.
For example I have a product selling for $100AUD (AUD being the base currency which is set).
A customer then want to purchase this product in Euros so they purchase it for 60 Euro.
I then check the order in the back end of the site and it is showing 100 Euro instead.
So it has switched the value with the base currency.
Any ideas?