Not sure it will help, but here is sort of what you are talking about:
http://core.trac.wordpress.org/ticket/14134
Try adding:
suhosin.post.max_vars = 5000
suhosin.request.max_vars = 5000
to your php.ini
Not sure it will help, but here is sort of what you are talking about:
http://core.trac.wordpress.org/ticket/14134
Try adding:
suhosin.post.max_vars = 5000
suhosin.request.max_vars = 5000
to your php.ini