If you are saying your total tolerance on the toolpath is 0.005 inch, that is way too loose. Tighten it up to something like 0.0001. If your machine chokes on the code, many of the toolpaths can be filtered down.
If you can, post up the SW file and the parasolid file. You could also put both files in an assembly and compare them.
Hi Matt thanks for taking the time to respond. The 0.005 is metric sorry I should have said. We are injection mould makers and have been manufacturing with mastercam for over 15 years now. This is a problem that has recently come up since I moved the design of the tooling on to solidworks, nearly all our tooling will have a draft angle of some sort which will not have any problems but recently we have made a few tools that have round sections which cannot have any draft angle for design reasons. This is where the problem has shown up. I will try comparing the two files to see what happens thanks for the tip. Also I'm new here so ill look at uploading the file to the server.