If you have non-ascii characters in your document then you ahve to make sure that you set the code-page correctly in the conversion settings. The '?' characters in the output represent characters that are unknown in the code page/font combination that has been set for the output document. Having said that, it is always possible that there are limitations in what Calibre can handle in RTF format!
The reason that it is probably working when you save as HTML is that the HTML document will have the correct code page set.
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