Hi Gerald,
This is a known issue - large gradebooks hit PHP's "max_input_vars" limit (which defaults to 1000), with subsequent fields simply not being passed on to the Moodle code by PHP. The quickest and easiest way to deal with it is to increase max_input_vars in your PHP configuration (assuming that you, or your administrator if that's not you, have access to do so; this may not be possible on shared hosting environments).
Recent Moodle 2 builds have various workarounds for the issue (with 2.3.5 and 2.4.2 being the most user-friendly so far: MDL-35074 ). If you're stuck on 1.9 and unable (or not willing) to increase max_input_vars, let me know and I'll provide you with a patch to implement that workaround on 1.9 (we're approaching the final stages of moving to Moodle 2 at the moment, so I had to implement it on our 1.9 site).
-Paul