You are getting this behavior because you broke one or several of the patch rules.
After having a diff between your target and upgraded .AIP files, it seems you changed the order of the .WAR file in the folder. Its GUID is also changed from one version to the next.
Advanced Installer strives to respect all the rules, but due to the involved complexity, success is not always guaranteed. Because of this it is recommended to use patches only for minor updates, that do not change the Product Code and to test the patch throughly in various installation scenarios.
A complete list of patch rules can be found here in Creating Patches article
All the best,