I'm not sure which version of Moodle you are using, but there have been a few problems in this area with 1.5. In fact a problem with webct import was fixed just today. If you are using 1.5, you should probably grab the latest stable branch (although wait until it is built again to incorporate the latest fix), or get the STABLE branch from CVS.
Failing that - upgrade to 1.5.2 and check the following post for the webct fix....