I had another customer who had (maybe) similar problem: he registered a lot of meta boxes and fields and couldn't save them. The problem was: PHP limits the number of POST fields, usually 1000, and also POST size. This makes you not save all fields when you build your meta boxes with the Builder.
Here are some links for reference about this:
http://stackoverflow.com/questions/8710185/new-limit-within-php-1000-fields-per-post-does-someone-know-if-the-number-can
http://www.inmotionhosting.com/support/community-support/prestashop-15/increase-the-maxinputvars-in-phpini
The fix for that is editing the .htaccess (or php.ini) like this:
php_value max_input_vars 3000
php_value suhosin.get.max_vars 3000
php_value suhosin.post.max_vars 3000
php_value suhosin.request.max_vars 3000
See here for more information: http://stackoverflow.com/a/14166562/371240
Please try and let us know if this fixes.
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