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. I tried to edit the config file for TortoiseSVN [Settings, Subversion configuration file: Edit] like this:

[auto-props]
### The format of the entries is:
###   file-name-pattern = propname[=value][;propname[=value]...]
### The file-name-pattern can contain wildcards (such as '*' and
### '?').  All entries which match will be applied to the file.
### Note that auto-props functionality must be enabled, which
### is typically done by setting the 'enable-auto-props' option.
makefile = svn:eol-style=LF
*.h = svn:eol-style=LF
*.F = svn:eol-style=LF
*.sh = svn:eol-style=LF
*.bash = svn:eol-style=LF
*.mk = svn:eol-style=LF
*.in = svn:eol-style=LF}}}

But it did not help. Plus, I am not sure whether this would mess up real Windows users if these file properties were transferred to the repository. I suspect the svn:eol-style=native that has been assigned in the repository overrides this, and "Native" means "Windows" to TortoiseSVN. Never had this problem before. 

So, like John, I will now mostly use the command line SVN.