This happens because windows is case insensitive and linux is case sensitive. As an example, in windows, the files "Foo", "FOO", and "foo" are all the same. It doesn't care about the caps on the names. In linux, "Foo", "FOO", and "foo" are totally different files, because the caps matters.
I suppose linux must default every windows file to lower case to keep all the names clean and consistent, but I can see how this might be annoying at times... not sure of an easy way to fix it, though..
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