By any chance to you have display of errors turned on? If you do can you turn off display errors and see if that corrects the problem? I you turn on error logging do you see any errors from ACF in the error log?
This is just a guess but there could be a PHP error during the AJAX request that’s that is triggered for ACF to check if the field groups should be active or not. If there is an error then basically all checks return false and that causes all of the field groups to be removed.
Let me know if you need more information about php error and the WP error log.
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