Do you get the "Could not resync" message when this happens? You shouldn't be able to edit in the compare window... editing is done in the main UI window then you re-load the file into the comparison window. Is this what you are referring to?
Yes, the axis orientation arrows look funny if you get the view rolled around so that you are looking it from below the zero plane. I could add a button or some other method to reset the isometric view orientation.
The macro translator has been updated a few times and I ended up leaving in the comments and block numbers just because its easy to remove them after the fact and I thought some folks would want them.