I have recently experienced problems with flickering ONLY when initiating shutdown via the desktop. The flicker starts as soon as the desaturate desktop procedure has finished. Occasionally I found some localised flicker, i.e in right hand corner only when minimising or closing via min and close buttons.
BUT by unchecking VSync in Desktops Effects the flickering has disappeared completely.

Some info,

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core/iasl 20110527-2 [installed]
    Intel ACPI Source Language compiler
core/ipw2100-fw 1.3-6 [installed]
    Intel Centrino Drivers firmware for IPW2100
core/ipw2200-fw 3.1-4 [installed]
    Firmware for the Intel PRO/Wireless 2200BG
platform/enblend-enfuse 4.0-2
    intelligent blend tool for overlapping picture
platform/intel-dri 8.0.3-2 [installed]
    Mesa DRI drivers for Intel
platform/libchewing 0.3.3-1
    Improved Smart Chewing Library - Intelligent Chinese Phonetic
    Input Method
platform/libva-driver-intel 1.0.15-2
    VA-API implementation for Intel G45 chipsets and Intel HD Graphics
    for Intel Core processor family.
platform/xf86-video-i740 1.3.3-2 (xorg-video-drivers)
    X.org Intel i740 video driver
platform/xf86-video-intel 2.19.0-2 (xorg-drivers xorg) [installed]
    X.org Intel i810/i830/i915/945G/G965+ video drivers


Currently on kde 4.9.1 here [Chakra testing] and using smaragd kwindeco. The flickering started on a fresh install; kde 4.9 and without smaragd or any other modifications made.
Please ask if more info is needed.
TIA

Further info,
Enabling VSync again and now disabling Logout in Desktop Effects cures the flicker also.
But this now causes screen tear with minimal movement at the top of the screen and the desktop background to display in greyscale and what appears as a tiled background.
Happy to provide information as required to help solve this...

My guess would be the combination of VSync and the Logout effect triggers a bug in the graphics drivers.
Does this occur with the default setup under a new user?

Thanks for your reply bcooksley,
This occurs with a fresh Chakra x86_64 install (KDE 4.9.0, Linux 3.4.6). Looking at this thread there are some similarities; namely full screen, VSync and tearing. In this same thread both Martin and Thomas say the issue is rectified in 4.9.1, however enabling [Testing] in Chakra upgrades to KDE 4.9.1 and Linux 3.4.6 without any improvement. I'm wondering if the fix was included in Chakra's release of 4.9.1 of 4 days ago.

I created a new user to be sure, with the same issues as above. I can try a clean install and see what that shows.

It seems the other user is also having the issue, even with KDE 4.9.1 as well. I would recommend joining that thread at this time, as the cause for both your problems is likely the same or similar.

Confirm the problem still exists on a fresh Chakra (2012.09.05 release) with Desktop Effects enabled the only user change.

I would recommend joining that thread at this time, as the cause for both your problems is likely the same or similar.

Thanks bcooksley, I'll join that thread from here...