I doubt you're still wrestling with this... but I just did and figured out the answer.
If you look in jsrt.h you'll see that all the native functions use a wchar_t when using string parameters, however the DllImport attribute doesn't specify the charset, so it defaults to ANSI.
I did a find/replace in the Native.cs file and changed all the DllImport attributes to read...
[DllImport("jscript9.dll", CharSet = CharSet.Unicode)]
... and now my code works fine. I've sent a pull request to the sample owner on GitHub to get this fixed up. The update is currently in my fork at https://github.com/billti/chakra-host