I know it’s been a while, but I’ve got the same issue. Googling “magento product compare” brought this up!
I’ve found the file which is causing the issue, but have no idea how to fix it:
app > design > frontend > base > template > catalog > product > compate > sidebare.phtml
If you rename the file, it removes both boxes but I cant see in the code where the duplicate is coming from?