The query you want to show as an example is:
SELECT * FROM temp WHERE mydate > '2009-06-29 16:00:44';
04:00:00 is 4AM, so all the results you're displaying come after that, which is correct.
If you want to show everything after 4PM, you need to use the correct (24hr) notation in your query.
To make things a bit clearer, try this:
SELECT mydate, DATE_FORMAT(mydate, '%r') FROM temp;
That will show you the date, and its 12hr time.