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It's possible that the database is getting somehow corrupted and that is why these actions aren't showing up, but it's also possible that you've simply configured something to hide them.

You can rebuild your database to check out the corruption theory. First, make a backup with File->Back Up Database... just so that you can show it to Omni if rebuilding the database solves your problem; maybe they'll be able to divine what was wrong. Then, do File->Rebuild Database... which will reconstruct the database cache and make sure that everything seems correct. If after doing that it still doesn't work, I would bet that the problem is not with the database but with, um, the operator :-)

I would bring up the view bar in context mode, and set it to All Contexts, Ungrouped, Project, Remaining, Any Duration, Any Flag. Make sure that both the Contexts and No Context bins are selected in the sidebar. Now search for the missing actions. Did they turn up?