Really hard to see how this would be related to Zotero. Do you see CPU peaking in Activity Monitor when sync takes place? If so, does your screen flicker when you do something else that is CPU intensive.

Yes, that's right, I mean the Zotero pane and it doesn't occur if I'm in another program, I believe. By 'flickering' I mean that the Zotero pane darkens and you see very briefly the little pop-up bar showing that Zotero is saving something.

I ran some more tests. It seems to only to occur when new information - such as a child note or a new item has been added to the library - is saved through the sync.

If I run actions more CPU intensive, there is no flickering.