Hello,
I assume that you are using XY mode to automate the menu. You can try to use special mode of normal recording mode instead. Press and hold "Ctrl+Shift" and do the actions with menu. When "Ctrl+Shift" is pressed WPM Recorder records ALL mouse actions, including MouseOver. You have to be careful what you do and only move mouse where you really need, but it should help with popup menus that require MouseOver events to open.
It may be good to first move mouse over menu element, then press "Ctrl+Shift", move mouse few pixels so that "Mouse over on ...." action is recorded for that element and then release "Ctrl+Shift". Repeat this selectively for all places where menu expects MouseOver event. This will limit number of extra actions to ones that are really needed.