Pathauto, [term-raw] and FCKEditor

Hi

I'm building a site using a single taxonomy that applies to some but not all content types. I've configured the Automated Alias Settings so that the path for a node using the taxonomy is:

[term-raw]/[title-raw]

When I create a node using one of those content types, the Pathauto correctly creates the path, e.g:

fishing/story-about-fishing

So far, so good.

The problem arises if I then manually insert a link into that node using FCKEditor where the link points to a node using a different taxonomy term. For example, the link might be:

boating/story-about-boating

When I save the node, the link is rewritten to be:

fishing/boating/story-about-boating

And, of course, this path doesn't exist. I can get around the problem by manually adding a new alias to point this path to the correct node, but that has two problems. First, it's manual and painful. Second, these links will be seen by search engines as duplicate content.

Is there any way to get around this? Can I override this behavious in FCKEditor, or is it nothing to do with FCKEditor?

Thanks

David