The Dock doesn't recognize applications

I have a problem that the Dock sometimes doesn't recognize that I've opened an application.
It doesn't show the little dot underneath the app in the Dock and the menus when pressing the application is also not correct since the application is open.
It can be everything from third party apps to Apples Mail app.
What can I do?

Nevermind, I found another thread about this. https://discussions.apple.com/thread/4150205?tstart=0

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I have noticed recently that the App folder in the dock doesn't contain all the apps in the main Applications folder (the correct one under Macintosh HD).
This occurs whether in list, grid, automatic or whatever.
I've removed the apps folder from the dock and dragged in the current one and yet it doesn't show all the apps from the source folder.
Any ideas on why this is happening or how I can fix it?
There are 55 items in the Apps folder but only 51 are shown in the folder located in the dock.
If I drag it over (as per normal operation), all 55 should appear right?
Is there a limit on how many can be displayed?
Can the grid spacing/icon size be changed to fit them all in if that's the case?
Just dunno why this is happening???
Cheers
Frank
Mac i5 / OS X 10.6.8

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http://support.apple.com/kb/HT4137
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Message was edited by: WZZZ

The Dock doesn't recognize applications

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