If you can email me the scene RTF content offlist I can check why this is happening. I remember fixing it once before, can't even remember what was causing it as it was indeed pretty obscure.
Open the scene, go to the Raw Markup tab, then select the raw rtf tab and also the generated RTF tab. It might be best if you send both.
Is your project in YW5, YW6 or YW7 format? Only the YW5 format saves and loads RTF, the other two translate it to internal markup from the scene window, and back to RTF again to display it.