I had/have a problem with a 6x9 diffuser Bimabox for my Durst. It took me a while to figure out where the problem lay and fortunately, I have more boxes so I was able to just switch.
However, during the elimination process, the problem certainly wasn't visible on the white base board with a negative in the holder nor was it obvious without a neg and not knowing about it.
I seriously can't remember if it was actually noticeable even knowing about it or by inspecting the box itself, it seemed so subtle. Replacing the white diffuser material would have been my next step. Come to think of it, I believe Durst supplied a diff.1 and a diff.2 diffuser panel, the thicker diff.2 specifically being for colour printing for better/more even light spread and consistency.
I know your enlarger is not a Durst but perhaps my experience might be helpful. I know how frustrating these kind of things can be! Best of luck.
Sorry, just to add, to switch between vertical and horizontal formats a couple of things need to change on my Durst L1200's but I have no idea if that's the case on your enlarger.