Checked your files and everything seems OK. You may want to change "Show available stock level in cart when less than order" to TRUE. It's your option, but if the customer places 5 in the cart and you only have 3 in stock - It will show so they don't have to guess how many they can buy.

Check your file products_with_attributes_stock.php on line 482.
If it reads echo '<div id="pwa-table"';
It IS MISSING >

It should read echo '<div id="pwa-table">';

This probably won't fix the other problem, but it sure fixes a lot of the "SYNC" and "SORT" problems.