Lion quarantine causing applications to not launch/open

Hello all,
I seem to have tripped over this quarantine bug in Lion. Newly downloaded apps simply sit in the Dock with the sphere pulsing, and disappear when clicked on.
I've found a few places that talk about possible workarounds with Terminal, but haven't been able to get them to work for me.
https://discussions.apple.com/message/17933033#17933033
https://discussions.apple.com/thread/3826648?tstart=0
http://reviews.cnet.com/8301-13727_7-57374676-263/workarounds-for-quarantine-bug -in-os-x-lion/
http://reviews.cnet.com/8301-13727_7-57406599-263/tackling-a-newly-installed-app lication-not-opening-in-os-x/
Is there anything new known about this situation? Is there any other workaround or trick to try? This is stopping me from being able to install any new software properly. I'm hoping I don't have to wipe the system and start over, but I'm not seeing much choice. Assuming I don't trip the bug during the rebuild process and end up back in the same spot....
Helpful pointers or information greatly appreciated,
Markie

Good questions, apologies for the vagueness.
Download app from 3rd party site, haven't confirmed if something from App Store has the same problem.
Copy app to Applications folder
Icon appears in the Dock with the plusing "I'm launching" sphere beneath it.
That's where it just hangs there, and clicking the icon in the Dock causes it to disappear and the launch to abort
I don't have an anti-virus running in the background, but I do periodically run ClamXav (about once a week).
I've tried uninstalling with AppCleaner
I've tried uninstalling manually
I've copied and replaced
I've emptied Trash, Logged out, restarted, tried the Terminal to flip quarantine bit workaround, etc -- all multiple times with no change in behavior
The App I'm currently battling with
MacTubes (http://macapps.sakura.ne.jp/mactubes/index_en.html)
I innocently updated from the previous (working) version just this morning and realized this had happened with another app last week.

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I recommend taking a look at this article named iTunes: Finding lost media and downloads found here http://support.apple.com/kb/ts1408
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