You would probably be best off taking a snapshot on a completely fresh system, instead of one that already has the software installed/ then uninstalled, then reinstalled on it. Easier for Composer to capture what files are being created during installation. I just have a second partition on my test machine that I reimage constantly to capture "clean" snapshots. For the most part, I just treat the partitions like two separate computers.
Also, if you haven't tried it, take a snapshot with new + modified files. Should give you more places to look and see what things are installed. Try snapshotting the old version of the software, too. Maybe it installs differently than the new version.
Note that not every file that is captured by a snapshot is something that needs to be in the new package. Some entries can be deleted, like system diagnostic logs.
When you have a snapshot, you can also select "Allow Package to be Uninstalled" within Casper Admin. This will search the target computer for all files included in the package, and then remove them.
You can then set up a policy to uninstall a package, instead of installing it. You can set that option on the Packages tab when creating a policy. It is only visible when the package you've added to the policy has been enabled for uninstallation. All the packages I make with Composer are output as .DMG files, don't know if that is required or not.
Yet another thing to consider is that the permissions on the application may have gotten messed up by copying from your computer to the target systems. I don't use ARD, but just copying things on the finder level will break a lot for me. The copied file will end up with the original account as the Owner of the file, and all other users have No Access to it. Check on one of your target systems with Get Info to see if that's the case. This can be fixed by issuing a chmod 755 command targeting the application. 755 allows for write privileges to admins, but everyone else can still read the file.
