In newer PHP-Versions the count of input-fileds per formula (POST) will be limited to 1000 (unverified information). It seams that this limit is already installed in certain
I too have come across this issue, working on a localised installation of my code, and Debian Sid has upgraded to 5.4 RC4 PHP. A form of over 7000 lines with checkboxes (!) suddenly only processed 1001 of these in the $_POST data...head scratching for a few hours.
Made the change in /etc/php5/apache2/php.ini:
max_input_vars = 5000
save, and restart apache, and it's all good now.