I have had a related problem under DNN 4.0.  I added an image module in the slogan pane and ticked the "Display module on all pages" box.  Then I deleted the module without unticking the box first, and later added a new image module, also ticking the "Display module on all pages" box.

Problem One:  On existing pages in the site *both* the deleted image module and the new image module now appear. If I untick the box, the second module disappears, but the original deleted one remained.   I was forced to go through every page in the site and manually delete the shadow instances of the original deleted module.

Problem Two:  Even with the box now unticked, each time I create a new page, the deleted original image module appears on the new page and must be manually deleted.

I found a reference to the tick/untick problem and shadow instances under DNN 3.2 in the bug database, but it was a problem with the "untick" not being recognized.  This is not the problem under 4.0.  I believe this is a bug, and would very much like to hear if anyone has a workaround.  Thanks.

I neglected to read carefully what krollb had written.  It seems as though deleting the module works to remove it from a page, though permanently removing it from all pages likely needs the solution I suggested -- unchecking on the original page.

Sorry I can't comment on your other issues.

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/Brian C