I have had a similar problem, as I use Subversion (well, really SVK) to shuttle files between my Linux and Windows machines. In Subversion, you need to set the svn:eol-style properties appropriately because it doesn't handle line ending conversions by default.
If that's what you're using, too, check out SubversionConfigurationForLineEndings
for how to set up a config file to automatically do this for you.
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