There are various pre-processing stages in the publishing engine and possibly one of those stages does not properly resolve the links.
What Oxygen version are you using? If you are using an external DITA Open Toolkit version, what version is that?
I looked in our email archive for discussions with you, found two of them, based on two different forum posts, but not on the "50606" post.
Could you possibly send us again a sample to reproduce the problem (email@example.com
Sorry for the inconvenience. Whenever we do not reply in 2-3 days please write us again, we either did not receive the email or there was some human error on our part.