What are you using for your menu provider?  Are you using a lot of CSS.  If you switch back to the default skin does everything work?

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-Mitchel Sellers
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I'm using a custom skin that I created for my project. I found the culprit but I don't know why it's doing it. In IE6 it creates iFrames for some reason and I found that there were two contrasting css settings being created with the js file dnn.dom.positioning.js. Whats strange to me though is that the inline style said display:none; and then there was another attribute of display:block; the display:block; was creating basically an invisible block over all of the content on the page. So no links or anything were clickable because this iFrame was covering it up. there was an iFrame that did this for every menuItem in the navigation as well as every module menuitem. The only way I could fix it was to removed the line in js file that set it to block. I have no css in my skin that has anything to do with iframes so I have no clue what actually caused it to do this.

 

Oh yea I'm using the dnn:Nav control with the updated WebControls version to allow UL listings. But the issue has been mainly with the DNNMenuProvider I think it was doing the same thing with the others but I don't remember now.