This may also be a case of Microstation/MX creating more than one Design Model in the process. Microstation can have more than one Design Models (Modelspace), while AutoCAD can only have one. When Exporting to DWG, there is a setting under Options -> Advanced for "Non-Default Design Models". The options are Ignore If Not Merged (Don't export them at all), Create Paper Space (does exactly that - makes them a layout tab instead of a model tab) or Create Separate Files (like it says, makes each Design model into it's own separate file). That's the option I think you want to use.
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