I was just testing out the hexagonal map and found that it looks exactly like the isometric (staggered). Is there a work-around to stop this?
The hexagonal grid only looks different from a staggered map if the Tile Side Length property of the map isn't left at 0. See also the topic introducing the hex support in Tiled:
I see now. You're only able to change the "hexsidelength" after you've created the map and not during the map setup.
Right, actually this is something I should fix. A field for entering this value, as well as a preview of the grid, should really be part of the New Map dialog.