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thx for the extra details, it took me some time to think about it…
I would like to propose a possible solution.
do you believe, whenever a corrupted image is detected, the creation/sending of that (partial or whole) frame could be skipped?
by what I was observing, the corruption may be a fully blank image for the specific window (or pseudo/non managed window), or a partially blank (fully transparent region of the) image for each application/plugin/panel.
Such workaround could be optional, and we could even add specific applications to not be checked for corruption, so if it messes something, the end user could still deal with it pointly.
I think it wont interfere on playing games framerate also, but if it ever do, we could just add such game application as an exception to be ignored for corruption, and/or to create/send all frames whenever such application is running.
Btw, the best framerates for games are only possible while using MetaCity(Gnome) window manager, AFAIK it has no 3D features.
Also, I found that KWin still flikers too (just much less often than compiz), and Mutter flickers everything even not having any transparency, so my guess is again that it is something related to a general 3D problem vs how NoMachine works.
(I cant find a button to edit the OP?)
As an anternative to Compiz(Unity3D) I am using KWin (that has 3D effects) + GnomePanel, this means that it is not a 3D graphics problem either, because the NoMachine is stable, no flickerings, using that alternative. So it seems to be a Unity3D only incompatibility.