The "Save as Rhino v5 file if opened as v5" was something I added in after MoI v3 so the next version of MoI would fix the problem reported here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=7166.1

It had to do with plug-in data extensions to materials only being written by OpenNURBS for v5 files and being ignored for v4 files.

But yes that will only be in effect in the next version of MoI, not MoI v3.

I had remembered something about that but I forgot that MoI v3 didn't do that yet.

- Michael