A family of Microsoft relational database management systems designed for ease of use.
I have had issues in the past with summary task % complete not updating, but I cannot duplicate now. As an experiment, take one of the milestone (zero duration) tasks and change the % complete to something other than 100%. Does the summary task % complete change? Set it back to 100% - any better?
Take a look at the tracking table - do all tasks have an actual finish date? Does pressing F9 fix it?