Unresponsive / WindowServer freezing on new iMac

Hello,
While editing images in Aperture, I am encountering frequent freezing.  Aperture becomes unresponsive for several seconds to half a minute or more, and then starts to respond again.  It has occured after using a few different types of brushes, but happens most consistently when I do skin smoothing.  When it freezes, the entire system is inaccessible -- I cannot switch to other applications or bring up the Dock.  Also, the mouse pointer does _not_ change to a beachball.
I am running Aperture 3.4.4 in Mountain Lion on a brand new 2012 iMac 27" 3.4 GHz with NVidia 680MX, 24GB ram and 1TB Fusion Drive.  My photos are on the Fusion dive and it has a lot of free space.  The photos are managed in the Aperture library (not referenced).
I checked the Console and the WindowServer is showing a lot of messages like this:
2013-04-27 4:52:13.191 PM WindowServer[108]: disable_update_likely_unbalanced: UI updates still disabled by application "Aperture" after 16.39 seconds (server forcibly re-enabled them after 1.00 seconds). Likely an unbalanced disableUpdate call.
2013-04-27 4:52:13.193 PM WindowServer[108]: reenable_update_for_connection: UI updates were finally reenabled by application "Aperture" after 16.39 seconds (server forcibly re-enabled them after 1.00 seconds)
2013-04-27 4:55:43.729 PM WindowServer[108]: CGXDisableUpdate: UI updates were forcibly disabled by application "Aperture" for over 1.00 seconds. Server has re-enabled them.
2013-04-27 4:55:43.735 PM WindowServer[108]: reenable_update_for_connection: UI updates were finally reenabled by application "Aperture" after 1.77 seconds (server forcibly re-enabled them after 1.76 seconds)
2013-04-27 5:03:35.832 PM WindowServer[108]: CGXDisableUpdate: UI updates were forcibly disabled by application "Aperture" for over 1.00 seconds. Server has re-enabled them.
2013-04-27 5:03:35.836 PM WindowServer[108]: reenable_update_for_connection: UI updates were finally reenabled by application "Aperture" after 38.18 seconds (server forcibly re-enabled them after 38.17 seconds)
2013-04-27 5:10:13.197 PM WindowServer[108]: CGXDisableUpdate: UI updates were forcibly disabled by application "Aperture" for over 1.00 seconds. Server has re-enabled them.
2013-04-27 5:10:14.633 PM WindowServer[108]: reenable_update_for_connection: UI updates were finally reenabled by application "Aperture" after 2.44 seconds (server forcibly re-enabled them after 1.00 seconds)
I tried the following:
1.  Disk Utilty repair permissions
2.  All three of Repair Permissions / Repair Database / Rebuild Database on my Aperture library
3.  Deleted Aperture preferences from ~/Library/Preferences/com.apple.Aperture.plist
4.  Deleted the Aperture cache from ~/Library/Caches/com.apple.Aperture and re-started.
Unfortunately the problem is still happening.  The new iMac seems to be working reliably in other applications and is a very fast machine.  I am at a loss for what else to do. 

Léonie,
Thanks for replying.   To summarize the steps Linc Davis suggested for diagnosis:
Step 1.  Log in under Guest account and see if problem occurs (to isolate whether it is localized to my user account).
Step 2.  Boot in Safe Mode and see if the problem occurs (to isolate whether it is caused by third party kernel extensions etc. installed on the system)
Step 3.  Run several terminal commands to list what third party extensions etc. are on the system.
Step 4.  Boot from a clean install of Mountain Lion on an external drive and see if the problem still occurs.
I will try Step 1 and Step 2 first and post back.
In the other thread, the user is encountering WindowServer freezes in many applications (Safari, Mail, Activity Monitor…).  So far for me, the problem is isolated to Aperture only.
Trevor

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    {------------ Please click the "White Kudos" Thumbs Up to say THANKS for helping.
    Please click the "Accept As Solution" on my post, if my assistance has solved your issue. ------------V
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