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The RTF plugin has seen a lot of changes recently, and work is still on-going. It was noted in the release notes some time back that this could cause regressions. If you have a file which no longer works, open a bug with the file - bugs.calibre-ebook.com. I expect it could get resolved quickly if a working test case is provided.
Outside of providing the developers with a file that demonstrates the problem, your only other option is to use MS Word to create filtered html.
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