This is a good question because a disparity between USMLE and COMLEX could speak to just a lot of variability in either performance, or computer tests validity in general. Frequently there are people who fail a step and then pass with a comment like "I was in a bad relationship, or a relative died, or I should have studied more for this but my MBA course was rough". We are asked to accept this explanation, so if these are valid explanations, we should ignore a discrepancy. I don't speak for all directors or at least shouldn't so much, but either through laziness or just the reasoning that no one accidentally kills a step, if you have done well at least once on a step, you probably successfully learned the material.
You could extrapolate this into failing a rotation and then remediating it, but this is a bigger deal. Particularly if the concerns were professionalism or communication. These aren't covered well on tests, although if someone has something it would be worth money.