Ok, in case anyone else has similar problems, below is the text of the mail I've just sent to John highlighting the problem with the mesh...
... There were a couple of problems that were making it go screwy.
First, you had a huge >4 sided polygon hidden away within the SubPatch. There was also a 2 sided polygon floating around in there also. I suspect that this may have been the remnant from the original template shape that you haven’t deleted. Having non SubPatch polygons coplanar with subpatches causes all kinds of nasty behaviour. Essentially, one thing you need to watch out for with LW is every time you perform any bevel, Boolean, knife, etc. be sure to also do a merge points followed by deleting any unwanted polygons that get created (usually the 2 pointers).
Secondly, there was a bunch of overlapping polygons in the area you were having trouble with. What I’ve done here is to move the object out of SubPatch mode so it’s a little easier to work with, and then manually moved the overlapping points around to open up the hole (using the drag tool – ‘Ctrl-T’). Once I’d got the hole open, it was just a case of trying to fill it. To do this, I manually created a couple of polygons rather than welding points using point selections and the create polygon tool (‘p’ key). Fixing it this way, you’ll end up with less points having 5 or more patch intersections than if I simply performed a weld – this gives a cleaner mesh.
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See the screenshot below to see what I did:
Step 1 - Original Mesh
Step 2 - Overlapping points shifted
Step 3 - Point selection for new poly
Step 4 - Two new polys created
Step 5 - The corrected mesh.