Color Shift since 10.9.3 when launching apps

Hi,
Since my Macbook Pro Retina updated to 10.9.3, almost all apps revert back to the system default color profile for the display rather than the calibrated one from Colormunki Photo (which worked fine until 10.9.2 and I even recalibrated to create a new profile and checked its integrity).
This makes photo editing in applications a nightmare because colors are off. Way off for reproduction proofing.
The profile works in a lot of Apple native applications but even small free third party applications revert back to the system default profile.
What to do?
My workflow came to a screeching halt when this happened. (Clean installs, NVRAM and SMC reset, Disk Utility and combo updaters all do not solve this).
Thanks for all your help.
Madison

What are you calling a clean install?   There is erase and install.  And why not erase and install and just return to 10.9.2?
Using the Restore install leaves you with old information from 10.9.3, unless you erase the disk first.
It appears that there is a bug with colorsync in 10.9.3.
https://discussions.apple.com/docs/DOC-7151

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