How to fix the warning 'This program might not have installed correctly'?

Windows 7/Vista  sometimes started throwing the warning dialog titled "Program Comparability Assistant" and the the warning dialog included the following message.
"This program might not have installed properly" and there were two options. 1) Reinstall using recommended settings. 2) This program installed correctly when customers double clicked on the installer executable that I had made and released to customers already.. Its was not a good time today for me and I did not know how to fix this problem immediately.

From msdn support website, I found that this warning message is thrown when the installer does not make any entry to the Add/Remove Programs, for example, the installer does not install an Uninstaller onto the control panel nor does it make a Windows Registry.

As a quick fix, see if following workarounds work for you.

•  There is a service called Program Compatibility Assistant Service under your Windows Services. You can see this when your type the command services.msc in your windows Run command.  Try stopping this service and changing the service setting from automatic to manual. Follow this link for more details or see how to disable this warning message.
• Writing the right install script can solve this. Find more information on this here.    
• Try adding a manifest file mentioning the supported OS as both Windows Vista and Windows 7.

Here is the link that will resolve the issue: http://msdn.microsoft.com/en-us/library/aa374191.aspx

I personally I did not like the way Microsoft is handling this computability issues with this windows executable. We can't ask our customers to go and disable the windows Program Compatibility Assist Service (PCAS) without knowing what are the side effects of disabling this service.  Not an acceptable work around. This warning message is never meant to be resolved by the end Windows customers. The warning puts customers into confused state. I'm yet to understand the exact root cause of this issue.

I had created Windows executable by a wrapper called Lanuch4j which made be difficult to resolve this issue. If anyone knows how to programmatically resolve the issue without disabling the windows service, please let me know.