I noticed a lot of pirates showing up randomly all over the map which drives me nuts. I looked at the export_descr_buildings file and noticed the hidden resource is present in the file but is nowhere listed in the descr_regions file. This is understandable in a release of this magnitude. The attached rar file has an updated descr_regions file which will prevent pirates from cropping up in the smaller lakes but will still allow them to appear in the largest lakes and all salt water seas.
Here are a few screenshots illustrating the pirate issue:
The file should be placed in the Program Files\Sega\Medieval II Total War\mods\EBII\data\world\maps\base folder. I do not believe it is save game compatible.