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Never mind. I found that one of the comparators was missing in the list. Hence no comparison was used and the relations were created because it had no way of checking the instance id's. I think it's odd that the step and transformation was saving with that missing. it's fairly easy to over look that.
The error was saying that, but did not specify "which" comparator and between which fields.
Cool.. well, answered myself this time, but thanks for the opportunity to share.