Diff tool is unrelated. No need for any external tools or plugins, it's PsPad itself that does the damage. I once got this on a plain TXT file without any syntax highlighting and without using any functions like search/replace, just plain manual text editing and then saving. Though it was a while ago, cca 2 years, no such issues with recent versions on such simple files, but it still occasionally happens on more complex files/with more complex editing.
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