Anyways I have learned good lesson now, transaction involving EUROs its better to get the amount directly in bank account instead of receving them in paypal and then again transfering to bank account. in my case i followed second one.
by doing first one, can save ~$30.00 each on a $1000.00 transaction.
Paypal is going to do what is their best interest. I live in Europe now and when I take money out of my US bank account, it takes a few days before the transaction hits my account. No matter what xe.com says when I withdraw the money, somehow my bank finds a lower exchange rate when it takes the money from my account.
But anyway, you did find the solution. Don't transfer money between banks in a foreign currency and not expect to get shorted.
they usually take a 2.5% fee for conversions, and it's normal to take these fees. if you're dealing heavily with euro/dollar and don't need the conversion, then just open up an bank account with that currency.