Okay so i got it working. Adding a navigation mesh for the first time was a little overwhelming.
I lowered the cell size, and decreased the radius of my smallest agent slightly, This produced much more nav mesh but the nav mesh was still patchy and not always connected where it should be.
I built a lot of bridges from a spline. I had remove the collision and add a convex collision ensuring that the accuracy was 0 and the max hull verts was 32. This allowed the collision to cover all the gaps between the planks. Some planks were widely spaced and the nav mesh had trouble connecting it. I also made sure that the collision for the bridge was set as simple as convex.
I have supports and other props that break up the collision on my bridges. I was able to combat this by remove the collision and adding a convex collision ensuring the accuracy was 1 and max hull verts was 32. I again used simple as convex and made sure that Can Ever Affect Navigation was turned off and has navigation data was turned off.
This seemed to sort it for me and hopefully helps someone else.