You know, I went through something like this a while back...I deleted everything Blackberry from my laptop, and reinstalled from scratch. I don't think you need to go that far overboard, but perhaps use Add/Remove Software to remove Desktop Manager AND Handheld Software, and then reinstall both?
I had the same happen while trying to instal Reqireless and some other 3rd party aps, I had to do a full uninstal, registry and all folders and pointers. Got the updated desktop software and now haven't a problem. Sorry I can't be of more help but this is what solved it for me.
The solution to this issue is VERY simple. You do not have the handheld loader files installed on your computer. You will need to download the .exe file from your carriers website and install the loader files. At that point, when you run App Loader, it will display the list of modules.