The DataWedge application did need to be disabled, (this can be done programmatically via the datawedge API from Motorola, Thanks Abdel for the hint here!).
https://docs.symbol.com/ReleaseNotes/Release%20Notes%20-%20DataWedge_3.3.htm
A little background on our Windows Mobile application for reference, we have a hardware singleton that contains interfaces for all hardware components and loads related types and assemblies via reflection. If we referenced types directly the code above worked.
The end solution ended up being to use the Symbol.Barcode library instead of Symbol.Barcode2.