It’s not a mystery. The 50 mm enlarger lens is simply too far from the image plane making the magnification too great.
Try an 80 mm enlarger lens. For example, an 80 mm f/5.6N EL Nikkor has an 55 mm flange distance, while the 50 mm f.2.8N has a 43 mm flange distance.
An 80 mm lens achieves 1:1 magnification when its rear nodal point is about 160 mm from the image plane (sensor). The flange distance of the 80 mm f5.6N EL Nikkor is 55 mm. So that places the lens flange about 135 mm from the sensor. That should be easily done with the PB4 or PB6 bellows unit. Other 80 mm enlarging lenses will have similar dimensions.
I posted earlier in this thread - and a lot seems to have happened since. Several viable solutions have been offered to what turns out to be quite a technical task.
Fwiw, I have a PB-4 bellows & PS-4 film holder. I've tried a range of enlarger lenses and micro-nikkors, and the most convenient, and effective option for this bellows is the Micro-Nikkor 60mm. As stated above, its great advantage over the 55mm lens is that it can focus to 1:1 ratio, whereas the 55mm cannot. But on the right bellows, the 55mm should work fine.
After reading this thread today, I very quickly took out the bellows and set it up with my D800, and 60mm lens. I just used a clip on desk lamp as a temporary light source. I would normally use a flash gun. I could easily shoot a 35mm slide, albeit a lousy out of focus slide, but it was what I had to hand. The first image attached is the rig set for very slightly wider than 1:1 to include the full slide frame. The second image shows the setup where the 35mm is significantly cropped into, producing a reproduction of greater than 1:1 ratio. That's the lens basically front pressed to the PS-4 holder. Btw I use a 62-52mm step-down ring to allow the PS-4 in-built compendium shade attach to the micro-nikkor's 62mm filter thread.
I think one of the hidden issues the OP has encountered is that the PB-6 bellows is clearly inferior to the PB-4 version. Its vintage is probably from the same era as the Micro-Nikkor 60mm (1990's), which is more flexible than the older 55mm version. I wonder if the 60mm lens and the PB-6 bellows were designed to better combine, whereas the more flexible PB-4 bellows could better combine with the equally older 55mm Micro-Nikkor. It's just a guess, but my sense is that Nikon were generally very diligent about how these accessories functioned together. Retrospectively combining equipment from different generations creates it own complexities, which this thread clearly evidences.
... And hey Presto, yet again I cannot post the images to Photrio! This happens every time. My three jpegs are 420KB, 383KB, and 104KB. I tried dragging, attaching, and every conceivable variant of the .jpg extension! I get messages saying the files are too big(!) or that they are not recognised as images(!)
I guess nothing's easy...
So here's a dropbox link:
www.dropbox.com