I do not have an activex plugin to test, but I believe that if you can hide the plugin behind an iframe. When you show your modal popup, create an empty iframe. Give it the same size as the popup, and show it in the same place, but with a lower one z-index. The iframe should display above the activex plugin, and your popup should display above the iframe.
I can verify that this method works to mask blocks <select />in IE6. I myself have not tested it with ActiveX controls, but Google tells me that it should work.
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