Many people have discovered that after they migrate to Native Mode that the MP doesn't work or that they clients don't receive advertisements.
This is a known issue that is being worked out. To solve the problem you should uninstall and reinstall the MP. I personally can't say that I have had this problem. We decided that if were going to take the leap to SCCM we would do it with both feet.
http://blogs.technet.com/wemd_ua_-_sms_writing_team/archive/2008/05/30/is-the-documentation-for-migrating-a-site-to-native-mode-missing-a-step-to-uninstall-reinstall-the-management-point.aspx
Granted I work in Higher Education so we don't have many of the same limitations that corporations face. Thank you Microsoft for giving us technology at a lower cost for easier adoption.
