I've been doing a lot of work on AutoCAD and Inventor 2009 this past week and I kept on hitting a side-by-side error when I tried to export from XP to Vista or Vista to Vista (curiously it worked from XP to XP.) After some work I've found what the problem is and thought I'd share this since I've seen people in the past asking bout side-by-side errors.
Simply put a side-by-side error occurs when a shared DLL isn't properly registered with the system, this can be a manifest issue or an environmental variable issue (like the path not getting saved so Windows doesn't know where the DLL is).
The biggest culprit for side-by-side errors is Microsoft's Visual C++ runtime missing from the OS, and in the case of SVS that runtime doesn't capture properly which leads to the side-by-side issue. If you install the Visual C++ redistribute (in AutoCAD's case it's 2005) to the base of the capture machine before you run your capture and then install the runtime on the import machine everything should work fine.
I suspect this is also the cause of side-by-side errors with Visual Studio when it's captured in a layer.