oh... I think I see the possible issue Steve. The strokes may not be forming a correctly closed object in the way they were put together with the hanging portions attached to the outlines (if that makes any sense).
there are a couple ways you could approach this... you could select all and delete the fills completely... then go under the object>path and select "outline strokes". This will make best use of what you have without starting over.
Once you do that you could get some pen tool practice by creating a new layer. Place this layer under the original layer in the layers palette (drag and drop). I would lock the top layer with the stroke and make sure bottom layer is selected. Use the pen tool and just create a rough shape that lies under your stroked shape on the top layer. Try to create the curves and points of the shapes but you have a little room to be off so don't worry about being perfect. Just close the shape and fill if not already with the green color. If it helps... you can do this with fill layer on top then when shape is closed... just drop that layer below stroke layer
You could then group both the fill shape and stroke shape to keep both together on same layer for placement if you wanted.
Or... you could the the existing paths but would probably take much more time and cause you more frustration in long run.
Or... you just start a new layer over existing image and draw your shapes again that made image... overlap them with the stroke... then use the "delete anchor point too" and "add anchor point tool" to create segments in the areas you don't need stroked and delete but then you might have to reconnect the intersecting areas again and more time
Paths seems to act funny sometimes when you include extra anchor points and segments that are not on the closing loop of the shape and I often try to avoid these situations.
I think considering the complex nature of the shape with the extra legs.. I would just go with outlining the strokes and creating new fill underneat. Might even use pathfinder to "unite" the whole stroke shape as one after outlining... its good habit to try to keep your shapes and number of points as simple as possible for editing and reproductiion if .ai files are used on the output but hope this gives you some ideas.