This is an unfortunate side effect of adding a max height on your table. I'd do two things. 1. Make your filter a type ahead (so it doesn't drop down) 2. LImit the number of rows shown before pagination - This will bring up the loading indicator.
Look at the display properties of the table. You probably have table scrolling turned off. But if you turn it back on you will discover some of the underlying checkboxes and properties are still turned on. Turn them all off and you will be golden.