I thought it might be a better idea to bring this issue to the main git, seeing how this may effect more than just one game. I ran xenia in administrator mode, and made sure all files had read-only unchecked, yet I still have write-access issues with this game in particular, Tenchu Z. this did not happen in a previous build and it seems to be a regression of some sort related to xbl sign in which was enabled in the last working build for this game?
As referenced in game compatibility:
Did Xenia ever emulate the HDD filesystem? Saints Row 1 doesn't see any HDDs.