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wow good work. Yeah that IE firefox issue sux. Last time we used a similar menu, we wound up choosing to use it Horizonatal. (In fact in a month or two we will be relaunching our site with that type of menu)The horizontal display of the menu, which you should be able to configure easily, would enable to place the call script directly in the theme,(where the headder links are now) and snap that layer down.
You've done much though. perhaps a style trick can get you going to get IE to read it as absolute positioned. For instance in your left column you might insert a transparent spacer image that is the same width size as the menu, thus insuring the menu does not overlap? And that the column is a fixed width...
hmm...I dunno..the specifics though just jumping in.
good luck and congrats so far....
add ok so I see in the theme the column width is set to be 160 THe menu looks more like 170 its a random guess here, but see what happens when you set the column to be 170 instead in the html...any difference? IE is dumb, firefox probably went with the flow..
If that doesnt help it must be an "absolute" position issue so common between these browsers. arg