I rarely see this when you are downloading just a few emails, but when its been a while and Outlook is pulling 500 emails (498 of them being spam is often my case) the trouble can occur.  Outlook allows you to check for emails from all your accounts at once, in groups your define, or individually.  If you have more than one account and you're experiencing the issue, I suggest that you perform a receive action on each account individually by pressing the down arrow to the right on Send/Receive toolbar button, hover over each account, then select inbox from the fly-out menu.

If you do discover that the problem is with just one of the account, and you can access that account via a web interface, I suggest you clean out the messages via the web first and then try the download again.

If you are going to go with the upgrade route instead of the Reinstall/Repair route (both have their advantages), you need to change when the installer removes existing versions.  Different versions of Wise for Windows Installer have different ways to get to this, but you need to go to the MSI Script section, and edit the installation sequence under the Execute Immediate section.  Look for the RemoveExistingProducts line item towards the bottom and move it up the list, no higher than the InstallValidate line item. 

This will result in the old version being uninstalled first, then the new version being installed.  Because the files from the old version are not present any longer, the new files will be placed as expected.