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I've a iMac Late 2009 model with latest version of MacOS High Sierra and there are screen glitches/flickering on normal desktop usage but not in safe mode.

Where is the problem?

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Safe mode disables almost all GPU acceleration and fancy features, so you have a system where either the GPU itself has failed or the drivers / part of the system that run accelerated and fancy features is corrupt or broken or buggy. The one quick triage step is to see if making a new user account also shows the error.

Assuming that you can’t just live with the artifacts and hope that the software update will fix them and assuming that you have a full backup of all the data and programs you need to reinstall, I would triage this further:

  1. Install a totally clean macOS to an extra hard drive as a quick test of the current updated system and the graphics hardware work all together. (Bonus points is you now have downloaded the installer and optionally run createinstallmedia for a bootable installer.)

Based on the results there, you might open a support ticket with the vendor or seek a repair if the issue persists on a totally new and updated install of the OS. Hopefully you can cure this in software, but the age of the GPU and the specifics of the failure could easily be what the beginning of what failing portions of the hardware looks like visually.

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