One problem could be related to how the data is transferred between unix and windows. In a windows text file, each line of data is terminated with a carriage return (CR) and line feed (LF). But in unix the line terminator is just a LF. I've had instances when someone ftp'ed files to me from windows to unix, and the files still contained the dos terminators (CRLF). That caused problems reading the data. On the infile statement, I added the option termstr=crlf so that SAS would recognize the dos terminators. Maybe that will work for you. I have a feeling that the embedded CR is affecting your output.
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