I will admit to using Open Office more than MS Office and making most of my presentations as no-linear html documents but...
I don't think the order of installation would be important, the importer is a standalone parser(?). Office '07 saw MS switch over to XML much more heavily in the documents formats. It might be this isn't helping.
Also the range of effects were changed and ppt files became much less backwards compatible (what a surprise that wasn't!). It might be one of these effects that's causing the problem.
Using a VM shouldn't give problems, I use a few as my house is littered with SUN boxes on Solaris and Linux.