Hi Slieser,
Thanks again for posting this. I've successfully reproduced and fixed the problem in the upcoming 1.32b release.
The issue is caused by NCrunch losing knowledge of the XAML file's original encoding when modifications are being passed through by the IDE. Therefore you'll only experience this problem if you modify the encoded .XAML file while NCrunch is running in the background. As a workaround, closing the editor window containing the XAML file and doing a disable/enable on NCrunch should allow the issue to correct itself after you've made a change. Alternatively you could restart your IDE.
I hope this helps.
Cheers,
Remco