It seems that when we try to create a report with more than one join we get the message:

One or more JOINs has been added or deleted since you last modified the default JOINs.  Please recheck the custom JOIN before running this request.

The joins used are the same as the ones setup in the relationship builder and there have been no changes made to these.  I assume the custom join is created when the data items are brought into a report.  As these items are in the same order as the joins in the relation table I do NOT understand this message or what to do to get rid of it.