Foreign currency reconciliation

We are having issues in reconciling our USD bank account with GL. We have a USD bank account and we sometimes pay  in USD. Our functional currency is CAD so the system converts USD in CAD once an invoice is created and then again when a payment is made. The difference betwenn the two days rate goes as profit/loss into a specific account. Till this point everything it ok, however, at the time of monthends once the bank statement  comes and the clerk tries to reconcile it with GL things dont match and the difference runs into millions. I tried translating CAD into USD