Hi jetblast - yes like OSTexo writes the problem is that your 2 curves are on slightly different planes, or maybe one of them wiggles around just a little bit instead of being totally flat.

Once you flatten it then it should solve your problem. One quick way to flatten it is to select both curves, then go to the Top view and then grab a corner of the edit frame and squish it down until you get "flat" snap engaged as shown here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=3378.4

Once you have flattened those 2 curves to be on one common plane then the extrude should work as you want.

- Michael