To answer your question: I can imagine that there can be a problem since an application will be able to convert a properly set IFC element (such as a Wall) to its own native element type when importing it.
I mean this is the basis of IFC: that different applications export to standard IFC Element Types and then other applications can import those IFC Element types into their own apllications and properly recreate the geomety and building information content.
To answer your problem:
Please watch this video:
http://www.youtube.com/watch?v=NpiAiyDXjZU
If shows that you can define custom IFC Properties at various levels of the IFC hierarchy.
So if you define a custom IFC PRopety for the IFCObject level, which is the topmost level, then that IFC Property will be available to every single construction element type as a selectable and usable IFC PRoperty.
YOu can then fill out this Property with your company data.
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