Looking at the source of JSZip, in the file jszip.js of the download package on their website, I noticed this line of code (line 661-662):
utf8encode : function (string) {
string = string.replace(/\r\n/g,"\n");
So it seems like that's your problem. Perhaps you could try commenting out line 662, I don't know why it's there, it may well break something else. It seems they copied the code from here, as per the url in the source.