I had some problems with the installer as well:
first, i installed it via Software Update. After looking into /Library/QuickTime/ i found out, all the plugins still displayed the old version number - they just didn't update. So, i put those plugins manually to the trash. But be careful and only thrash those plugins, that get reinstalled by Apples installer (see http://support.apple.com/kb/DL1396 for more details).
I then downloaded the standalone installer from http://support.apple.com/kb/DL1396 and ran it. After that i made sure, all plugins in /Library/QuickTime/ were back there in their latest version. And voilá... all there.
Additionally, run Disk Utility afterwards and repair permissions. On my Mac, it corrected several wrong permissions related to the installed files.
This happens if you try to use the installer to install the codecs but do not have Final Cut installed. You have to unpackage the package and install the codecs manually, as described at http://www.jonathangrubbs.com/journal/pro-quicktime-codecs-no-fcp/
HERE is the solution sent to me by another Apple Community supporter:
I also had a similar problem to most people here. Cannot playback XDCAM files after upgrading from 10.5.8 to Snow Leopard 10.6.8. I called Apple who suggested a fresh install of Snow Leopard without upgrading the 'ProApps QuickTime Codecs 1.0.3' and copy the contents of the Library/QuickTime form the fresh install into my QT library. However, I decided to seek the file(s) that is the cause which is the AppleHDV.Component file. I copied the faulty one to my desktop (so I had a backup) and downloaed:
PerianXDCam.component.zip -> PerianXDCam.component
PerianHDV.component.zip -> PerianHDV.component
from this website: http://blog.lib.umn.edu/mcfa0086/discretecosine/164630.html
Once unzipped, copy into the Library/QuickTime folder and this should solve your problem, until Apple and Sony resolve this issue.