you tried to exchange the bitstamp to BTC-e with BitInstant or back with aurumXchange? if with aurum you're paying a double fee instead of just converting directly to the btc-e from your source funds
I tried to exchange using aurum again. As a matter of fact at that time fee for two conversions was actually lower than directly converting from mtgox to btc-e.
EDIT: Got response from support and my problem is solved.