How to prevent "This program might not have installed correctly" messages on Vista
Include this section in the program's manifest file:
<compatibility xmlns="urn:schemas-microsoft-com:compatibility.v1">
<application>
<!--The ID below indicates application support for Windows Vista -->
<supportedOS Id="{e2011457-1546-43c5-a5fe-008deee3d3f0}"/>
<!--The ID below indicates application support for Windows 7 -->
<supportedOS Id="{35138b9a-5d96-4fbd-8e2d-a2440225f93a}"/>
<!--The ID below indicates application support for Windows 8 -->
<supportedOS Id="{4a2f28e3-53b9-4441-ba9c-d69d4a4a6e38}"/>
<!--The ID below indicates application support for Windows 8.1 -->
<supportedOS Id="{1f676c76-80e1-4239-95bb-83d0f6d0da78}"/>
<!--The ID below indicates application support for Windows 10 -->
<supportedOS Id="{8e0f7a12-bfb3-4fe8-b9a5-48fd50a15a9a}"/>
</application>
</compatibility>
It'll suppress Program Compatibility Assistant by stating that your app is compatible with Vista and Win 7.
You need to add some information into the AppCompat section of the registry.
See this link and look for "How to disable a Program Compatibility Assistant warning".
Also there is apparently a method that involves adding a manifest file to your setup executable to flag it as "Vista-aware".
The first thing you should try is to add a "Vista manifest" with requestedExecutionLevel
If that is not enough (Clicking cancel on uninstall with UAC off etc) you need to use undocumented stuff like setting the image version field in the PE header to 6.0
One of the reasons that this message pops up is when the system thinks you're running an installer but it doesn't find an entry for the application in the add/remove programs list.
I don't know if this is the case for your app, but it's worth checking.