I have been having problems with the "working" issue where desktop manager sticks in this mode. To fix it I toss the Blackberry folder in Docs and Settings on my PC and all is fine until I want to add another program or update one. The installer insists on removing most of my third party apps even though I don't want to. How can I stop it from doing this as there is no option to not remove "unrecognized" software. Any way to install apps without using the desktop manager?

It's a good question.
It's a problem for me when I install programs from two separate desktops, each only recognizing the software they've installed.

Make sure all your programs/Software is checked. If you uncheck them, they will be removed.

Well, found the answer on the forums. Just wasn't searching for the right stuff. Here is what you need to do:
"You probably have the .alx and .cod files installed in different places. So apploader won't recognize them each time you start it up. I install them in \Program Files\Common Files\Research in Motion\Shared\Loader Files. I'm willing to bet if you don't install them there, you load them up just fine, but the next time you plug your bb in to install something else, it's not on the application list, if you manually add it back each time it will work also, but putting them in loader files will ensure they will be there the next time you install an app."
If you put the files there they will be added to the list of checked files and removed from the list of things to be removed.

I believe I wrote that. Anyhow, I have since learned that simply placing them in that location will not put them in the add/remove list without first manually adding it (Add button). Anytime after that, they will show up and won't remove it without your unchecking the box, so long as you don't delete the folder.

...and it really doesn't need to go into the Loader Files directory, but thats just to get it out of your way so you won't delete it (which is the case if you put the files on your desktop).

There is a folder under the BlackBerry folder that saves your loader history. If you delete that folder, then you will not have those optional components by default in the list when you run application loader.

I'd troubleshoot the "working" state to solve it and remove future hassles. If you are on a BES, one thing you can try is creating a new MAPI profile, open up the redirector settings, under Advanced should be a button to switch the mail profile...choose the new MAPI profile. "working" basically means that it's trying to connect to the mail server.

Zro