There is a documented bug with IE6 where select boxes ignore z-index, and this bug makes it so that popups in IE6 get mangled when placed on top of a page with select boxes. There is a related core issue that goes into more detail, #32862: Autocomplete.js popup appears behind SELECT elements in IE6.

What I used in my case was http://plugins.jquery.com/project/bgiframe (which MIT and GPL licensed). I include this .js file in popups.module and then in popups.js I add $popup.bgiframe(); in the Popups.open function. I also had to disable the overlay for IE6 because select boxes were showing through that and adding bgiframe() to the overlay made it completely opaque.

I'm sure IE6 compatibility is pretty far down the list of priorities on this module, maybe even worth setting to Won't Fix as that core issue was, but I needed it and perhaps others will. If this technique isn't too horrible I can attach a patch.