This is an odd problem, though luckily has a workaround for now. When trying to submit a job to Render Manager by browsing for the .max file, the Scene Manager states may be out of date. Common things we can see in the job submission dialog are incorrect frame paths and frame ranges, though I suspect all settings may be affected. If you submit the job from an open copy of Max, however, you will see the correct job settings.
Let me know if you have any questions, I can probably provide a sample scene if needed.