When using the InnoDB storage engine there is a bug that causes all the weight options to be set to "do not consider" every time the plugin's options page is loaded. This is a particularly large bug as it completely deactivates YARPP by simply visiting its options page in the WordPress Admin.
The solution is to change line 65 of the options.php to:
$weight = yarpp_get_option('weight');
Originally this line was:
$weight = yarpp_set_option('weight');
The "set" is a typo which causes an options array to be saved with weight => null.