When I set it up I told it to use unix style line endings, it seemed the least confusing of all the options.
I suggest you disable autocrlf in the config (should be in "%GIT_DIR%/etc/gitconfig"). If you use an editor that keeps line endings as they are, you should be fine.
The first time I had just used the github website and that is probably what brought up the crlf issue. Now that I've got a local copy, I plan on using ConTEXT do any edits/additions. I would think that it leaves the line endings as they are, but I don't really know...
I found the gifconfig file. Took a wild guess and forced it to open with ConTEXT (no extension so Windows won't automatically let me open it). It's a basic text file, and the autoCRLF is set to input. Do I just replace 'input' with 'disable' or is there something else that I should enter? I'd rather get it done right, than do something wrong and screw things up later...