This comment contains one serious point, a little technical information and a long ramble. Hope you don't mind :-)
First, if kickstart does choke on files just because of the extra <CR> after editing in the "other" operating system, I think it should probably be fixed. Shouldn't take too much to treat the extraneous <CR> as white space.
The precise difference is that /.*n.x/ systems use just Line Feed <LF> as a line terminator and DOS/Windows use Carriage Return, Line Feed <CR><LF>.
In fact the DOS version is more archaic. <CR><LF> comes from the days of mechanical terminals, and paper tape. The first files I ever dealt with were on paper tape - as a slip of a lad I was taught to strip down and rebuild Creed 12B teleprinters. We used to have what would now be called ASCII art, but it was in Baudot code on five hole tape, and these files would be printed by running them straight through the reader on the teleprinter.
<CR> comes first because it initiates the fly-back of the print head, and then the <LF> feeds the paper while the head is returning. This worked OK on a Creed at 50 baud (6.6 characters per second) but when switching up to 75 baud it didn't give enough time, and the first letter of the next line would get printed as a smudge somewhere towards the left hand end of the flyback, so wireless operators were always taught to use <CR><CR><LF> - and maybe throw in a "Letter shift" as well (Baudot code had to use two shift codes as a mode switch from Letter to Symbol).
It was similar technology that was originally used to interface to computers, hence the fact that early Operating Systems would have expected <CR><LF> (yes, I know about Hollerith cards - used those too :).
End of rant. Hope it was interesting.
Just a note, there is no "probably linux messed up with the file format" issue here. Any *NIX variant treats linefeeds differently than DOS based utilites. What happens is DOS based utilites put different control characters at the end of text lines than *NIX utilities do. For as long as it has been this way, to expect a text file edited on a windows machine to appear as expected on a *NIX machine is not even in the realm of reasonable. Furthermore, since *NIX systems have been around much longer than DOS based systems, I'd say that "probably Windows messed up with the file format"...
But thats just me :)
Aside from all that, I'm glad you were able to figure it out and get things going. Have fun :)