Icons stay in dock / Dock out of sync

Hi,
this one has been bugging me for many many months now (and as such is clearly not related to ML). Not sure if it was there with Snow Leopard as well but I already had it with Lion.
Things start going wrong on my MBP after several hours to days after a reboot. As far as I can tell it only happens after putting the MBP to sleep and waking it up but not always. The problem then is that the dock is out of sync. Newly opened programs are not being shown in the dock. Applications that are open and shown in the dock remain in the dock when closed. When I then click the corresponding icon in the dock the icon disappears. The only solution I have found to the problem so far is a reboot after which the problem is gone immediately (until it starts happening again several sleep/power on cycles later).
I am using Hyperdock and Totalfinder. Not sure if this is related. Has anyone here seen a similiar behaviour?
Kind regards,
JP

I checked their website and the only reference I found was it works with "10.6+", but maybe you're right.
Off topic, if you like TotalFinder you should try this, it's incredible:
http://cocoatech.com/pathfinder/
Back to business though. If you just want to knock this out, I'd make a new account really quick, log into it, and see how the dock behaves with no additional software running. If it works, great, we know it's the third party stuff. If it doesn't, we look into something else. Just delete the account afterwards.
And make sure you don't enable the stuff on the other account.
Also, delete the sleep image. Might help, I've had weird bugs fixed with it. When your computer goes to sleep it saves the contents of RAM on the hard drive to restore from. You know how sometimes when you open it up you get the grey screen with the bars filling up as your computer comes back on? That's what it's loading from. It might not do anything but you did mention it happening after it comes back from sleep.
1. Open a (normal) finder window.
2. Hit Command+Shift+G to open a popup where you can enter a location.
3. Paste in "/private/var/vm/" without the quotes, hit enter.
4. It should load a folder with a file called "sleepimage" and a few "swapfile" files.
5. Delete the sleepimage one, but nothing else. If you drag it to trash, make sure to empty the trash.

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To view your folder contents as you wish, right-click on the icon and choose the view options -
"display as" 'folder' will just show the folder, 'Stack' will show the first application in the folder (usually Adress Book).
View contenta as - list or grid - no fan option when the Dock's at the side (as it sounds like yours is).
EDIT
Incidentally, if you've dragged an alias to the Dock instead of the actual folder from Finder, you now have an alias pointing to another alias pointing to the Applications folder.
Bit unnecesary.
Message was edited by: noondaywitch

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Icons stay in dock / Dock out of sync

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