Do you have svn:eol-style set? If so, what is its value?
You mentioned Notepad++, which is Windows-only. On *NIX, the default EOL marker is n (LF), while on Windows its CRLF (rn). If svn:eol-style is set to native, when you check out on Windows the EOLs will be CRLF, and when you check out on *NIX, itll be LF - a difference of one byte per line. Visually, theres no difference. But there will be a checksum difference.
In Notepad++, turn on Show Whitespace Characters (I forget the exact wording, and am not in front of Windows at the moment). Do the same on a *NIX machine and your text editor of choice there. You should see a difference there.