Hi Erich,
To be honest I've never used MonoDevelop on Windows and have no intentions to start. I use the latest Mono VMWare image with OpenSuse (on thefree VMWare player), I get the code with Mercurial, and then I build mojoportal.mono.sln using MonoDevelop on Linux.I've never had any problems about choosing a platform, maybe that is an issue only on Windows. For .NET code we don't target specific processors, when compiling mojoPortal code in MonoDevelop we are only compiling to MSIL which is platform neutral and the runtime compiles that down to native code, so typically in .NET development we don't have to worry about the processor.
Hope it helps,
Joe