Visual studio also compiles with vbc.exe. So, the question you must ask yourself is what are the differences in my file compiled in the IDE and with codedom and how do I find them. If you decompile both apps using a combination of Reflector and Ildasm and the compare utility for notepad++ you should be able to find all the differences between your 2 files, then figure out how to make codedom compile with the same settings.
This will probably take you a few hours but you will learn a lot and you can create a nice dynamic generation of your binary without the issues you are having.
This will probably take you a few hours but you will learn a lot and you can create a nice dynamic generation of your binary without the issues you are having.