Graphic bug? Fault?

Since you now indicate that the project plays normally on the timeline and only upon rendering all does it show the issue, I would suggest 2 things.

1. Don't render anything, just export and see if the resulting file is OK. If not;
2. Close FCPX. Locate your library. Right click and open the library. Choose "Show Package contents". Drag the RENDER folder to the trash and also the ANALYSIS folder if you have used stabilization, etc. Empty the trash. REBOOT and the launch FCPX. Export your file first unrendered to see if the squares are still there. Then, if you want, try to render the timeline with Render ALL and try Render selection to see if that function is restored.

If that still doesn't work, repeat step 2 but this time clear FCPX preferences after the REBOOT and during the launching of FCPX by holding down Option and Command as you start the app.

Make sure you have a complete backup of your library before doing the above.

FYI - Disc Warrior is a drive utility application made by ALSOFT. I would try the above suggestion before uninstalling or reinstalling/repairing anything as it is relatively harmless and can be done very quickly.

Success, and a result...

Finally, I have success, a 3minute video file devoid of purple squares, and yes I think it is a bug.

As 4 of the clips are the same, I created a "save effects preset" of my chroma-key and applied it to all 4 or 5 clips that needed that effect, and on some of the clips it worked, and some it did not, it made the purple squares, either on the timeline or when I shared the video.

After disabling every clip in the timeline, and sharing the timeline turning on each clip in the timeline I was able to figure out the problem, so I removed the chroma-key effect, saved the green screen as a share, replaced each chromoa key with the standard one, shared out, and it worked.

Making a preset chroma-key as a preset seems buggy, or at least it did for me.

To test if it was hardware, which was my first concern, I re-edited something I knew was safe, it rendered no purple squares, so I ruled out the laptop, then embarked in hope of finding the suspect. There is always a suspect.

The purple squares meant something, it was too defined to be a random creation, purple squares with black dots, it was this that led me to think it was software, and not hardware, the re-edit of known good, proved hardware safe.

After changing all the chroma-key, rendering and sharing was again fast on the project that has bugged me for a week, so tomorrow I am going to show the production house, what the problem was, and what it was that solved the problem.

After 6 days of almost 14 hour days trying to find the problem, it is found, all I can say is thank you to everyone that contributed, one thing I am grateful for is not having to re-install anything....I am going to leave well alone!!

"replaced each chromoa key with the standard one"

Where you using a keyer plugin besides the built-in one?

What I meant was I replaced the one I created as a saved pre-set, and manually set each chroma-key. The save as effect seems to be buggy, something did not save correctly, but in the end, after countless ideas and efforts, finally solved!!

Feedback page. In a week or so I'm going to be compositing a ton of green screen stuff. Will be interesting to see what happens.

My advice, do a test "save effect as preset", treat it as unstable until you can confirm for yourself it is stable, that I mean using the built-in chroma-key along with cropping, and saving as a preset.

For me I am going to manually edit the chroma-key on each occasion I need it, for now I simply cannot trust the "save effect as preset" yet.

Actually, I'd manually key every shot no matter what. Things change over time, even in the same room/set over a couple of hours of shooting. But I'll test it in a few weeks as a preset, see what happens.