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I'm not sure of any freeware solutions off hand, but I do know of Emailchemy. It should be able to convert your .eml to .mbox no problem (someone even comments on it doing so). While not free it does offer a demo(it just masks sender&title fields on converted emails) so you can at least try it.

And just a thought.. I have no files to test with, but did you try importing it in Mail.app?


EDIT: Ok did a little more searching and found another way as well through a ruby script via Terminal called eml2mbox. It's free and you just need Ruby installed for it to work (I do believe OS X comes with a version of it).
 
olm to mbox

I got to this post trying to finally migrate away from the last microsoft product I am using.. outlook 2011. via menu the damn thing only let's you export .olm (which is pretty much useless), but you can drag n drop to export mbox format.
 
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