What program are you using to manipulate/check the text file? If you use Word, you can click to paragraph icon in the menu bar to display formatting codes such as spaces and line breaks. I've found in working with files sent to me by other people that there is some kind of "soft" line break that displays a different code symbol than a hard line break. I have never figured out what creates these "soft" line breaks, because I have never EVER seen one show up in any document that I have created -- but they exist, and may be related to your problem.
I'm still using Word 2003. For me, the "display formatting codes" icon is a typical backwards 'P' paragraph symbol that shows up on the upper menu bar, right next to the window for the zoom level. If you use Word 2007 or 2010, I don't know where the icon will be but I'm sure display codes is still available.
{Edit to add} Now y'all got me curious, so I went searching. The funky symbol I sometimes encounter is a "manual line break," and it's created by the combination of SHIFT+ENTER. The symbol that appears on screen for this is an 'L' shaped arrow, such as appears on many ENTER keys (what a coincidence!). In a relatively simple Word document, it seems to behave the same as a standard line break but it may do other things if it's in a file that gets imported into a different application.