Is the setting not persistent? (I assume you're using a Mac, since Windows doesn't support GPU acceleration — and many Mac users report glitchy operation when it's active.)
I don't Mac, but try the same thing as for all other InDesign working settings: with ID loaded but no document open, change the setting. If it's at all document-specific, that should permanently set the default to off.
Go to InDesign's Preferences > GPU Performance and uncheck it there. That should stick. Once you do that, the toggle under View greys out and cannot be changed unless you reactivate GPU performance.
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