After some experimenting, I can conclude that you must use the mwarray.dll specific to the 'bittyness' of the application you are running. To get both versions of mwarray.dll, I installed both versions (32 bit / 64 bit) of either the MCR or matlab. If you analyze the mwarray.dll assembly, it's been built as "Any CPU". Don't let that fool you - you need the correct bit version.
You don't need to build your NE Builder .net assembly in both 32 and 64 bit versions of Matlab NE Builder. I'm building with 64 bit matlab and it works on 32 bit systems.