I ran the Defraggler program on a Windows XP computer with the AS-400 PC5250 emulation program already installed. I restarted the computer and the user logged in and started their AS-400 session ok. The next day the AS-400 program would not start and the error message was that a bunch of AS-400 related .DLL files were missing. Tried to uninstall the AS-400 program and it would not uninstall or allow the AS-400 program to be reinstalled over the previous As-400 emulation program.
I am concerened and would like to know of any users that have had the same problems. I am thinking that the Windows XP operating shell was "kluged" by the Defraggler program. I am not installing the Defraggler program on any more computers until this issue is resolved.
You state that this is a defraggler issue. yet you say that everything was fine and usable after the defrag, it wasn't until the following day the issue showed up.
You also could mention the AS-400 emulation program, Client Access is the main one from IBM, yet others have BOS and a number of others. It is strange that you cannot do an uninstall, does it show up in add/remove ? (Notes: you might use the Revo Uninstaller for this rather than the one in CCleaner, since it is designed to clean up some extra stuff beyond add/remove. I think there also is a hunter mode for programs not in add/remove although another possibility is that the program has an uninstaller that is not registered in add/remove, then you use that.) Also the safe mode idea is good.)
However I also am not convinced that Defraggler was the issue, as far as I know it works through the Windows API so it would have a hard time losing any files . Especially 'later' rather than immediately. Make sure you do some checking in Event Viewer and try to see if there is any other sensitive programs doing stuff on the puter. And maybe check with the emulation vendor if they do anything special with file placement (although some of those companies are mostly orphan now in support, since Client Access is so capable and folks use it and Navigator). You do not mention any discussions with the vendor.
Keep in mind that most of the PC folks are not involved in AS/400 emulation, so that part of the discussion will sound Greek.