What's you mean 'file not found'?.
If your all php (standard, php53s and phpXYm) already have latest configure, no reason to appear error.
Running cleanup (not cleanup-simple or cleanup-norestart) also phpXYz-installer (change XY to 52-55 and z to s or m) will be fixed all issue. Yes, except if you have wrong config file (let say, in /etc/php-fpm.d/ exists 'alien' file) or still using 'old' custom file(s).