The problem (not sure if the only one, but for me it worked afterwards) is in the sorting function using in usort() in init.php file. When you’ve got more than 1000 cell inputs they are numbered in “1,xxx” manner. The sorting function – sortByOrder – uses function intval, that parses “1,xxx” as 1, which makes the mess. Just somehow force the value to parse in a correct way (get rid of the “,” by str_replace or something) and you should be ok.
