it can depends on o.s. I did tests on Fedora 14. and for patching without warning I had to use dos2unix tool.
Hmmm. I use a Linux Ubuntu laptop, so generating DOS end of lines is unlikely if it is not there at the beginning. Running "dos2unix" on the patch file locally does not seem to change anything. So I assume that the patch encoding was changed somewhere along the path you used to get it.