I don't think Microsoft has copyright on the whole of the OS/2 source code, just components they developed. I don't know for sure, but I think it is likely that some components, such as SOM or WPS, contain very little or no Microsoft-developed code. New features developed after OS/2 2.x were developed solely by IBM, without Microsoft involvement – Microsoft was only involved in OS/2 1.x (and possibly earlier stages of 2.x development.) There might also be some components which IBM licensed from third parties (non-Microsoft), but they are likely just individual DLLs or drivers, easily separated from the rest of the code.

I think the real problem here is IBM, not Microsoft or any other third-party. There are significant sections of the OS/2 code which are only under IBM's copyright, and there is nothing legally stopping IBM from supplying the source code to those sections, but it doesn't want to. Also, regarding the sections co-owned by Microsoft, I wonder what the story is – did IBM ask Microsoft and get told "No" (or "Yes" but only under non-viable conditions)? Or did IBM never even bother to ask Microsoft about it? I have no idea, but my gut tells me the later may be more likely than the former.