This usually happens when number of inputs(form fields) on your page is higher then allowed number of input by your server. 


Problem get solved in most of such cases by increasing max_input_vars . 


Newer versions of PHP implement a php.ini directive called max_input_vars usually set to 1000. This means that posting > 1000 form fields for instance would be truncated  preventing data from being saved.

This can be changed in php.ini file  

max_input_vars = 2000


If you are on shared host you can increase it via .htaccess file


php_value max_input_vars 2000


If you are not familiar with php.ini or .htaccess files ,open a ticket with your host and tell them to increase max_input_vars in php.ini file. 


Read more on this here

http://docs.woothemes.com/document/problems-with-large-amounts-of-data-not-saving-variations-rates-etc/