Winmerge comparisons and whitespace?

[countingsheep]

I am comparing files for an upgrade, and when I do, I get entire directories that show the files are different, yet, when I view the files, I see nothing different unless I select the option to view whitespace then it shows an extra space at the end of the line of code.. at least that is what I see?.. is that something that is crucial that I change? or can I filter that out to be ignored?

[DrByte]

Your files have likely been downloaded and saved with different line-endings than originally issued. This often happens with FTP programs translating from unix to windoze and vice-versa. You can probably prevent your FTP program from doing that by changing settings within it.
You can also tell WinMerge to ignore line-ending differences when doing comparisons.

[countingsheep]

I have the option off for viewing line differences, but it still shows a difference of some kind. Is there something else that I am missing? Or am I just the lucky one who gets sites that are all jacked up?