Welcome aboard, Reef.
Do you have the documentation for Neundo? Its a pretty pricey program and not many folks around here use it. I have Cubase SX2, though, and from what I understand they are fairly similar.
Are you recording to the 32 bit floating point .WAV? If so, you may need to dither to 24 bit for your mix. I doubt that's the only issue at hand, though.
Are you using any effects on the master channel?
Also check the export dialog box- If I recall there are a bunch of options to include or exclude effects and automation- make sure they are all included.
Good luck,
Chris