I would like to chime in.
After YEARS of having this issue I finally found this thread.
For me it was 39 fields, meaning ACF didn’t count past 38.
The only way I could fix this was by manually changing values in the custom fields column.
By adding the line
php_value max_input_vars 3000
to my .htaccess I was able to correct this.
Thank you for sharing this.
