As I had previously read about problems with the DLL.XML file here on the forum, I made a backup copy of my dll.xml file prior to uninstalling 1.2.
The installer will automatically do a backup, creating a file named "DLL_XML_Before_Addon_Manager.xml" in the same folder.
This dll.xml file was working perfectly well.
Can you please send me your backup (the backup you made or the one made by the installer) via email ? It's important I can reproduce the problem. Since many users do not have any problems, it's clear that there must be a specific case when the installer can't update the file correctly. There's no chance we can fix it, without having a sample XML to test.
Seems to me that there is a problem with either the uninstall of 1.2 or the install of the 1.3.
You can easily verify if the problem is in the 1.3 installer or it was in the 1.2 uninstaller, by simply installing 1.3 again. If the problem is in 1.3, it should repeat exactly. If it was in the 1.2 uninstaller, then we shouldn't worry, since that is no more.
But please, before making other tests, send me your backup via email. Address is on the "Contact Us" page.