Hi,
This is very likely to be due to your PHP settings.
Because it's a big list, it's likely that the setting max_input_vars (in PHP 5.5) or suhosin.post_max_vars (or something like that, in PHP 5.4) is blocking the users above 1000.
This is because the max_input_vars setting has a default of 1000, and because this page contains a bit more "input variables" than just this list of users (a few hidden fields and so on), you're probably left with just 967 users (1000 - 33 other fields or something like that).
Please try increasing this limit in your php.ini or you vhost config to 10,000, for example, and try again the same process.
Note that this error is likely to happen in all similar lists in Chamilo. It's simply a limit that is not often crossed in the 31,000 Chamilo portals we have around the globe, but around 5% of these are probably facing the problem at some point.
I'll add this to our optimization guide (in the documentation/ folder of your chamilo installation).
Please make sure you test that this Tuesday so we know for sure if this solves it or if there is something more, as we would like to release 1.10.6 on Wednesday or so.