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50mm Nikon enlarger lenses

Your Nikkor is a 50 - your Rodenstock is an 80, and is only using the center of the lens when printing 35mm negs. You're comparing apples to oranges here.

But I'd check alignment first. I'm a little spoiled with a Versalab Parallel ($200-ish bucks, worth every penny) - there are many way to check enlarger alignment, but the laser is wicked fast.

If you can only get one portion of the neg in focus, alignment is the first thing that will come to many minds.
 
I too had a similar problem with two El Nikkors. The problem was due to a misaligned mounting ring on the lensboard which I had purchased 2nd hand. Even visually I could see the lens was tilting cockeyed which I didn't notice until after hours of printing and cursing.
 
But the distance of the 80mm from the baseboard is greater than the 50mm, so misalignment should still be evident. I think the culprit is the turret.
 
A three lens turret introduces one more possibility for problems.

Very true. When I first got it, I noticed that the spinning part of the turret doesn't quite spin perfectly. It wobbles a bit so I had to shim it.
 
f/16 is awfully small for a 50mm enlarging lens. Fine grain is less sharp at f/8 than at f/5.6 with the EL-Nikkor f/2.8 that I uaually used. However, smoothing out grain might add to some photos.
This is one of those things you have to do for oneself; compare 16x20 prints with the Nikkor 50, side-by-side at various apertures. Yes as f16 is approached, the center of the print grain becomes more indistinct, but the corners (which were blurry without any grain showing) sharpen up to match the grain at the center. Yes, f16 is unbearable under a grain focuser, but in a 16x20 print it can be very acceptable if done right. Worked for me in graduate school when a Schneider High Magnification lens was not available and my enlarger column would not go high enough to print a 16x20 with an 80mm lens.
 
Since the problem does not occur when you change lenses, could it be the lensboard somehow? What happens when you close the lens a couple of stops?
Good idea;the depth of field during enlarging is relatively wide and should bring the entire neg eslily into acceptable focus.
 
A report on my Nikkor 50mm enlarger lens. I discovered that my enlarger is out of alignment.

I haven't used it close to a year. Since I don't live where my darkroom is, I'll have to realign it next weekend. It's really strange how enlargers get out of alignment when no one uses it. I've had my Beseler 45MT for over 30 years and it served me well. Time for a little TLC for my old friend.
 

I'm glad you have the problem narrowed down. I've had the same issue with my 50mm Nikkor on a Beseler 23. I keep it aligned now with a laser tool which I can't remember the name of. It's been six months since I've printed anything so I'll need to check and clean everything before the fall printing season starts for me.
 
They're great. I work in a university art department and they have one. It uses mirrors too. The tool is an expensive one trick pony so I prefer to borrow it instead.