Hum.. Sounds like possibly Line Breaks as well. After all .pdf files are just text files. Although if there are some images in there, that may cause in issue.
Make sure that you are setting your like breaks correctly as well. On the Windows OS its: \r\n and on Unix/Linux its: \n. It's \r on Macintosh systems incause you're curious :)
If there are no images in the PDF file, then you are fine. If there are, then make sure you use binmode. It sounds like binmode isn't an issue cause it works on your linux system. The next thing is to play with your line breaks. Set $\ to "\r\n" on the windows system and "\n" on the linux system (Perl defaults to "\n").
Better yet, take a look at the file on the WinNT box. You may have \n in there, so you just need to convert "\n" to "\r\n" to get it working.
A couple things for ya to try out ;)
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