Are you able to post any code samples with the difference between implementation of your compiled C# RegEx class and your wrapper call?
Unfortunately no, as all of this code is client-owned. However, I only used simple matching, there is nothing fancy there.
Without seeing the code it would be almost pointless to investigate the issue, can you not recreate the issue in a sample app.
one huge difference is that the body of text you are searching will have been pushed into unmanged memory...