Wmode transparent causes MCs to disappear

I’ve seen only a couple of threads on this topic and no one had a solution, but here is my problem: I have several movieclips that contain text boxes with filters on them (drop shadow). When I export the movie normally it works fine, but when its live on our site our jQuery menu gets covered up by it in IE.

When I add in the embed param wmode=“transparent” the menu works correctly (comes in over the top of the movie) but the MCs that had filters applied to them complete disappear. Does anyone know how to fix this?