I seem to be answering all my own questions...
I found the solution to my problem.
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With the expanding nested menu, the config file (*.ini for php, *.js for html) has a css position attribute in there. It is set to 'absolute' by default. I just had to make it 'relative', and everything worked like a charm.
Code:
//navbar orientation
$um['orientation'] = array(
'vertical', // alignment ["vertical"|"horizontal"|"popup"|"expanding"]
'left', // h align ["left"|"right"]
'top', // v align ["top"|"bottom"]
'absolute', // positioning ["relative"|"absolute"|"fixed"|"allfixed"]
'0.5em', // x position ["em"|"ex"|"px"|"0"]
'0.5em', // y position ["em"|"ex"|"px"|"0"]
'1000' // z order ["0" to "10000"] (menu takes 20000 headroom)
);
Change the parameter above to relative, and it works~
I was stupid not to think of this earlier.