I never had this problem before, but caught a bad case today.

I have Cygwin operating in "Unix" mode, which means it does not want DOS CR/LF end-of-line.

I just demonstrated to myself that the latest version of TortoiseSVN messes up the files so they won't compile under Cygwin, but using SVN from the command line did not. So, like John, I will now mostly use the command line SVN.