Apple ProRes422 glitches in quicktime but smooth in final cut. Glitches on export. HELP!

Do you playback the video from an external disk?

I think what hyphen was asking was did you store your output clip on your computer's internal hard drive or do you have an external hard drive attached to your computer of additional storage. This is totally different than video from the internet. Where you store your footage can be critical under some circumstances.

And don't stress; if you followed good practice procedures when you set up your project it's unlikely anything will be lost.

You don't mention which Mac you're using and that can make a big difference when you play back high-bandwidth video files. If (for example) you're using the internal disk on a MacBook (which frequently has the slower 5400 RPM disk) then playback might suffer. Playback from a an additional disk in a Mac Pro would be much less likely to to so.

Be aware that while Final Cut Pro 7 doesn't like the Canon 5D Mk3 footage as it is written, QuickTime is fine with it. QT doesn't have to deal with all the editing issues, so it can do a better playback job, so if you're having playback problems with QT, it may not be the clip but something else like the hard drive.

It is always best to have your video source files on a different disk for best playback, so if you're cutting on a laptop or iMac you should have an external drive dedicated to this function and it should be attached via a fast connection (FireWire 800 or faster). If you are using a Mac Pro you can use either an internal or external drive as long as it satisfies the speed requirements.

Please post back your Mac model, OS version, configuration, and anything else that you think might help the diagnosis.

hope this helps

Can you post the youtube link?

Here's some generic advice: as per RatVega make sure that all your material, captured or transferred clips, render files and exported videos are on an external drive. The faster the better. Some times render files get corrupt. Delete them and after rendering again, export a new video. The same for projects. Start a new projects with the settings you desire and copy paste the edited material from the sequence of the old project to the sequence of the new one. The sequence will probably have to be rendered again. Once done export you video again. Does the problem persist?

Some times effects make cause problems such as yours. Does the stutter occur on parts where you applied special effects?