Curiosity question - why are you pasting so much text into yWriter? Obviously you're not using yWriter's scene editor for doing your actual writing - why is that?
Have you tried using the external editor for your pasting into the yWriter scenes? Right click a scene and click Open content with default RTF editor. This will open the scene in whichever word processor Windows defaults to for RTF files, as set in your Windows default programs. This may also give you a way to fix any scenes that have the strikethrough problem. Just remember after you save and close the scene to unlock it using the Finished with external editor option.
In general, the Visual Studio RTF control that Simon uses in yWriter has similar capabilities and limitations to WordPad.
It would be interesting to know whether pasting into WordPad gives you the same results as pasting into yWriter. It sounds like there's something in your source program that the Windows clipboard is bringing across that the RTF control doesn't properly interpret. What program are you copying from?
Dave Shaw