The only thing i can think of is either you have blown memory for the query or exceeded the time limit ...
To start with could you edit the run.php file and put at the top in the code
ini_set('memory_limit','200M'); // For example to see if this raises the amount of rows returned
set_time_limit ( 60 ) ; // Increase default time limit?
If you arent getting errors in web logs then try the following to see if that helps
I do have a report which produces over a million rows but this is using a setting 1G of memory.
See if that helps, otherwise you might need to see display