There should be no difference between the 90mm and the 135mm if the image on the easel is the same size and the aperture is also the same. That's true for a diffusion enlarger. I don't know how it works with a condenser. My guess would be you didn't switch condensers when you switched lens, but that's just a guess.

But in either case you will get much sharper results if you don't stop down so far. Try f/11 or f/8. If your enlarger is aligned you don't need much depth of field.