Multiple comments:
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Mysterious!
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The way you do stimulus presentation timing is about as unreliable and suboptimal as it could possibly get. Please look at our demos and tutorials how to do this properly.
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VRR mode for fine-grained timing – apart from requiring you to follow step 2 - **will not work with the amdgpu-pro driver ** as i explained to you about 1.5 months ago here:
XOrgConfCreator not prompting VRR settings for fine-grained visual stimulation timing
so it isn’t surprising that that does nothing. -
Without a simple self-contained script that shows in detail what your are doing, and that somebody can easily run on their Linux setup, this sounds hopeless to diagnose.
That said, if you wanted me to give it a try, your lab would have to buy priority support, as this sounds like something intricate and time consuming, easily eating up an hour of work.
-mario