Also known as “PHP is acting weird in QNAP web server”. Apparently PHP OPcache is causing 60s delay in page refresh, see php.ini settings below.

[opcache]
opcache.memory_consumption = 64
opcache.interned_strings_buffer = 8
opcache.max_accelerated_files = 4000
opcache.revalidate_freq = 60
opcache.fast_shutdown = 1

Solution is quite simple and it worked for my device!

Go to php.ini (Control Panel >Web Server >php.ini Maintenance > Edit )
Find opcache.fast_shutdown = 1 and below it add

opcache.enable = 0
opcache.validate_timestamps = 0

That should do the trick!
Thanks to Artand.