The recent update to FCP X does, in fact, add a new Pro Res format, called Pro Res 4444 XQ. It is (apparently) the highest clarity Prores codec released to date, aimed squarely at high end broadcast and cinema professionals. Arri has announced that their new Alexa cameras will all support the new format.
The press release says:
ProRes 4444 XQ has a higher target data rate of 500Mbps that makes it the ideal choice for post production that requires visual effects processing or extreme colour grading.
“ProRes 4444 XQ is a fantastic choice for high-end mastering and archiving,” added Henning Rädlein, Arri’s head of Digital Workflow Solutions. “ProRes 4444 XQ offers 12-bit RGB encoding with a low compression ratio of 1:4.5 that maintains the superior tonal range of Log C, while providing the speed, ease of use and familiarity of ProRes.
You can just install the codecs from this update:
But they are automatically installed with the latest updates to FCPX, Compressor and Motion. As far as I can see, the new codec is only available in Compressor X - I can't seem to access it through any other software, including After Effects, Media Encoder or legacy Apple software.
That said, I have the updates installed on the machine I'm using and don't seem to have any other Quicktime issues, other than no access to the new ProRes format. Sorry I can't offer more help.