App aliases beep when launched from Dock

Recently, my rMBP has started beeping (System Alert) when I launch apps that are aliases from the Dock.  If I just put the app in the Dock, no alert when launching it.  But if I make an alias of an app (say, for a collection of apps, like the Adobe Suite, or Internet related apps) in a folder, and drag the folder to the Dock so that I can launch any of the apps in that collection, the app will launch, but I get the beep/System Alert.  For the life of me I can't figure out why, and it only recently started doing this in the last month or so...was fine before.  I can't figure out why, and haven't had any luck Googling the issue.  Has anyone had this happen to them before, or have an idea what could be causing it?

From my experience playing with the Thrive, when you attempt to watch a media file, it will open a menu asking you what application to use. From that popup, you can set a default.
- Peter

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