I experienced the same problems a few years ago and I was using good enlarging lens on a Zone VI VC Cold Cathode enlarger and thought that I had my enlarger correctly aligned. I tried every remedy mentioned here but it was not until I invested in a quality lens alignment system, the Versilab Laser tool, that I cured the problem.
It takes less than 2 minutes to check the alignment and it is sharp from corner to corner every time. I have also noticed that the alignment can shift as the head is moved up and down the column so for that reason I check the alignment for every print that I make if I have moved the head on the column. The initial investment for the tool may seem to be high but in my view if you are looking for the best results you should be prepared to spend the money, I believe there is no other way.