So, there seems to be two issues you are reporting:
1) I first copied my 2012 install to a new folder so that I can still run the 2012 alongside the 2013. On the 2013 install, in the System Tools - Software Uninstaller, I notice that none of my tags showed from my 2012 install - all other areas of the 2013 install show my previous tags.
The tags are stored in the TagSystem.dat file. Did you copy that from the old installation to the new, in order to import the tags?
Additionally, there are FAR fewer entries displayed in the Software Installer - entries that should most definitely be there as they do appear in the Windows 8 Programs and Features. When I run the 2012, all things still look good.
Could you send here a screenshot of the Windows 8 Program and Features and the Software Uninstaller, and the Software.log file from the installation directory of jv16 PowerTools 2013? Note: You might not be able to upload the log file here as it is, it may need to be zipped first.
