If that's a decompiled version of pass_timbertown, I'm pretty sure it's caused because of misplaced areaportals; it's a common issue when decompiling the map. I may be wrong accusing areaportals but I'd still like to point out their issue on decompiled maps.
As for the removal of skip/hint brushes, you should go to the VisGroups>Auto, hide everything by un-checking "Auto" and only check either "Hint" or "Skip"; either choice will automatically check both. Lastly, use the mouse in a 2D-view window, mark everything and press Enter to select all these brushes and remove them. Don't use the "Select All" option from "Edit" as it will select everything in your map, even the hidden objects.
This method ensures the removal of any Skip/Hint textures in the map so you don't miss any. You should also save the Hint-less version of the map with a different filename for tesing purposes.