I have been trying to improve the performance of my Geoserver installation (on xenial 64-bit), so I installed JAI and ImageIO as described here: http://geoserver.geo-solutions.it/edu/en/install_run/jai_io_install.html. Things went fine, and in the server status page Geoserver says that native JAI and Image IO are present (true). The WMS seems faster now, and the JAI memory usage is > 0, so I know it's in use.
I am serving single-band, uncompressed GeoTiff hillshades that I have prepared with inner tiling and overviews, which are 1-2gb in size.
But now I have this issue: at some zoom levels, there are gaps and unrendered sections. It doesn't even seem to be on a per-tile basis, as you can see below.
So it seems like this drawing issue is related to JAI and Image IO, because this same tif draws fine on my other instance which doesn't have those libraries installed natively.
edit: This is GeoServer 2.11.1.
edit 2: The GeoTiffs are in Web Mercator so Geoserver is not doing any reprojection. I am using Leaflet on the front end.