PyCharm behavior inconsistent with command line ironpython

I have an ironpython script which I am launching in pycharm. The script imports custom c# assemblies and employs classes found within. Everything is fine when this script is launched at command line. The problem comes when I try to launch the script in pycharm. I get an error like this:

SystemError: Could not load file or assembly 'great_assembly.dll' or one of its dependencies.  is not a valid Win32 application. (Exception from HRESULT: 0x800700C1)

This comes from the line I pasted below. This line is just retrieving a path (string) from a settings object.

clr.AddReferenceToFileAndPath(self.settings.__getitem__('greatAssembly'))

The run configuration is perfectly standard. It has all default settings. It is using the proper interpreter (IPY 2.7). Anyone have any idea why this might show up in pycharm but not at command line?