I had the same problem with 1.93. I renamed (and changed the contents of) a file called "hdr.xml" to "HDR.xml", set the FixCaseRenames option to false, and it continued to insist that I really meant "hdr.xml". I updated to 1.10 and restarted hoping that reloading it would fix the problem, but alas it still wants to force me to use lower case when I try to make a patch.
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