When you create a multi line entry in e.g. the cash receipt journal in NAV 5.1  and happen to have the same customer in two lines (customer might be paying with two checks).  If you go to apply entries on the second line after applying on the first one, the system filters on your applies ID and the document number, not the line number.  Therefore the totals include the previous application, which throws the system off a little.  You can still post without a problem.

 An easy fix to this would be to account for the line number as well as the document no when going to the applies to screen.