Looks like you have menu items intended for the two-column style (with the search being in the middle), but used in a single column style. This can happen if you upgrade from version 3.6.8 to 4.0.2 while you are using a custom skin with no option for single/double column. In that case the settings upgrade cannot determine conclusively if the skin has one or two columns, and assumes one.
The easiest solution is to go to the Customize Start Menu tab, right-click on the left column and choose "Reset Start Menu".
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