you ARE reading the file line by line and I don't think any other method is going to make a difference because the end of the line is DEFINED by the presence of a CR and thus if you have a CR any method that reads line by line will see a new line at the CR.

I think you'll either need to get rid of the CR as it goes INTO the file, not as you read the file, or else you're going to have to spot some other clue on how you parse the file.