Hello everyone. I ran into this issue too last night and found this post. This morning I tried putting it into a new HTML page all by itself and I still had the same effect. I was not able to draw a Polygon Hotspot. Then I realzed that my image's alignment was set to RIGHT. I changed it to default and magic, the Polygon Tool worked! I even tried that approach on the original page which is all CSS divs and same thing - changed the Alignment to Default - used the Polygon Hotspot Tool - then switched it back to Right Align and all was good. Perhaps this will help you all.
I have been having the same problem in CS3 - the accessablility pop-up box appears leaving you with only a dot and two coords. Same problem whether it was within or outside a div or table.
But I found that turning off the accessibility pop-up for images solved the problem - to begin with, only if the image was outside a div. You have to copy the map coords accross, and then if you are lucky it might trigger the thing to start working.
Dont ya just love it - chick-a-boom!