Programs do not move from drive to drive gracefully, more or less by design. Consider yourself lucky that the operating system didn't suffer from similar problems from this process.
For future reference, the best method for moving programs from drive to drive, is to uninstall and then reinstall.
I installed a 250GB SATA 7200 RPM Western Digital HD today. I used the software that came with it (Data Lifeguard Tools) to set it up as the main drive, and then use the old hard drive for storage. The software partitioned the new drive and copied the files over from the old HD. The old HD still has all of the files on it. Here is my problem: All of my programs are acting like it is the first time they have run. My Zone Alarm Firewall settings were reset. I tried to play Madden 07 and it said some files were missing and it needed uninstalled and then reinstalled, but no saved data would be lost. I did that and it started to play just like normal, but as the game is loading past the "EA Sports" tagline, the game crashes. Help!