It would be the PHP setting max_input_vars that could restrict the number of results you get. And, if you have suhosin, there are settings for that which would do the same (I'm not sure about mod_security, but I would guess so with that also).
Did you ever say what version of PHP and MySQL are on the server?
Did you ever ask your host if they changed anything on your server at about the time this problem started?
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