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First off, check and make sure that the modules are installed. If the modules aren't installed, the system won't recgonize them. To install modules, go to the module administration page.
If the modules you are having problems with are installed, try this. With the system Main Menu block, only modules that the user has permission to view will show up in the block. Verify that users have permission to view the modules, especially Anonymous Users, who typically aren't granted access by default.
If this doesn't help the situation, verify that the order # for the modules you are having problems with are not set to zero. It's possible that the values were not submitted to the database.
If none of these solutions alleviate the problem, feel free to post back.
Well, I hope that helps! Good luck with your site!
-zimmi88 =)
"Need coffee, keep away..."