Un-force-quittable app? It's not running, but it is, but it isn't

I have an app that got caught in some sort of endless loop... it didn't freeze, it just sat there spinning a progress indicator for about 36 hours when I tried opening a file. I'm not getting the wait cursor, the menus are pop open when I click on them, all options on them are just disabled, and the "quit" option is grayed out. It's like being stuck in a modal dialog box. So finally I force quit the app. But it's still in my dock. I hold the mouse button down on the dock icon, and it gices me the force quit option, which does nothing, and the app icon stays in the dock as if the program is still running. The activity amnager and the terminal's ps command both say the app isn't running. When I go to the app icon in finder and double click it, I get a message that the application "cannot be launched" with no further info. The kill command in terminal doesn't work because the app isn't running. Even though it is. Even though it isn't.
I can NOT restart my machine right now, I have a very large non-resumable download going in in the background, I expect it to take until tomorrow to finish.
Why would an app behave like this? How do I stop this insanity? Ay ay ay, I am soooooooooooooooooooooooooooooooooooooooooo sick of troubleshooting. Anyone know what I should do?
Thanks in advance,
Mike
Message was edited by: Mike K (edited to tone down the frustration level)

You could try these two options in Applescript:
tell application "Dock" to quit
tell application "Finder" to quit

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