On install I copy some files in 'System32' folder. When uninstalling these files are not deleted. Why?
How did the files get to that folder - manually? if so they will not be deleted, see http://kb.acresso.com/selfservice/viewContent.do?externalID=Q100225
I am using InstallScript and there are certain function that will rollback on uninstall: InstallScript Functions that Are Logged for Uninstallation - They mention there it applies also for InstallScript or InstallScript MSI projects.
Is this an MSI based install or installscript? If MSI, maybe the verbose log will give some more insight? Also (you probably checked) but make sure those files aren't marked as Permanent.
Also, is this a dynamic linked file or static? I sometimes have issues with dynamic because of missing keyfiles with msi based installers. You might try and make the files statically linked.
MSI Installations are supposed to be declarative rather than procedural. You declare what files should be copied and they get copied by windows installer. When uninstalling Windows Installer knows which files to delete, because it, because he did install them in the first place.
On the other hand if you make something manual during installation, like copying files yourself, Windows Installer doesn't know about this and it is your responsibility to delete them when uninstalling.