I have an issue in MS Project Professional 2010 - and not using Server 2010. It occurs when I have saved as 2003-2007, made changes, and re-saved. (And, I have set the File-->Options-->Saving option to always save as the old version, and when I get asked at 'Auto Saves' if I want to save, I select "no" as dialog directs so that it saves in old version format.)
When I re-open my project (saved as 2003-2007 format), random tasks have "disappeared" leaving a blank row where they used to be - however, I always find them showing after the last task in the project plan. They won't have changed (if you had predecessors set even the start and stop dates are still as entered). You just end up having to move them back up to the blank row.
I have not seen this problem when I leave in MS Proj 2010 format - only when I am saving to old versions of MS Project.