thanks for the question.
My assumption here is that you are affected by an issue that happens with some server configurations. Certain server extensions (like the "Suhosin" security extension), and recently even a change in the PHP default configuration can lead to this kind of problem.
What happens is this: When a large table is edited and saved, its contents are sent in a HTTP POST request to the server. If the table now has many cells, these extensions on the server think (wrongly) that something is wrong, and thus modify or sometimes even block the request.
And the request modification is what likely happened here: Due to the high number of cells, the server just "lost" the values for the checkboxes (like "Table Head" and so on). And this basically deactivates all the features, like sorting and so on.
Unfortunately, this can't really be fixed in WP-Table Reloaded (due to the internal data format). However there is a solution: I'm currently working on the official an designated successor of WP-Table Reloaded, called TablePress. That new plugin has the same (and more and better) features as WP-Table Reloaded, but due to an entirely new internal structure, it can use a much better saving process (using JSON and AJAX, if you have heard about that). And with that new saving process, the issues you are experiencing are history :-)
So, my suggestion here is that you switch to TablePress, which is available at http://wordpress.org/extend/plugins/tablepress/ (It's currently in beta stage, but it already very stable.) There's also more information available on how to quickly migrate from WP-Table Reloaded to TablePress at http://tablepress.org/migration-from-wp-table-reloaded/