The main cause of this is the Suhosin module that is bundled in some PHP versions (mainly hardened PHP version). This module basically limits the amount of input variables that can be posted within a form, so if you have a form with alot of textboxes or dropdown boxes, like the variation section when adding/editing a product, then there is a good chance that this limit will be reached and therefore the whole form will not be processed.
Firstly you will need to ask your hosting provider to see if you do have the Suhosin module OR you can run the phpinfo() PHP function and just search for 'Suhosin'. If you do have this module then you can either disable it or extend the limit. To do this you will need to add in some php_value settings in your .htaccess file. This you will definitely need to ask you hosting provider to see if you do have permission to add this in. If you do not and you do add in the php_value setting then this will result in the 'Internal Server Error' error page to show up when you access your site.
These are the php_value setting that you will need to put in your .htaccess file:
php_value suhosin.request.max_vars 20000
php_value suhosin.post.max_vars 20000
This will set the limit to 20000, so you will not be able to submit a form with more than 20000 input variables, which this limit should never be reached (if it did then the form would take a long to to submit all those input variables). You can also use 0 instead of 20000 which will effectly disable that check, but this has varying results.
