I'm afraid I don't really have the answer, I can only find a few cases in general like you describe and no answer for them. It is surprising that you can reproduce it on your desktop machine.
One thing you could try is a third party iFilter.
http://www.ifiltershop.com/msgfilter.html The desktop version is free for non commercial use so you can try it out and see, if you are willing.
Otherwise I'm pretty much out of ideas, we've seen that the iFilter is used, it's just how it's working that is wrong. I suppose the "index properties and file contents" option we talked about before is a good lead, perhaps somehow that setting (however it is persisted on the system) is just not applying to the iFilter that is loading from the ifilter test application or search.
-your feedback is helpful to other users, thank you!
