I understand your confusion about PB Value and grade. A similar situation exists between Mussina and Johnson. About the only explaination I can come up with is that RJ's abymsal hitting stats: (10 failed BHA for instance) and 91 PA significantly detract from his PB value.

Compare Mussina v. Mays and I think you can make a stronger arguement for radical PB value differences being hard to explain. Stat wise very even with two notable exceptions: Mussina walks less 42/228.2 and strikes out more 214/228.2
than Mays 64/233.2 and 123/233.2. Given that both are AL guys and had virtually no PA, (Mussina had 7 and Mays 1) One could argue that Mussina should have a better grade but not a better clutch number as Mays was much better with runners in scoring position .597 OPS v .773 OPS for Mussina.

Also Mays had a slightly higher overall OPS .654 than Mussina OPS .632 Given Mussina's dominance in walks allowed, strikeout ratio, dongs allowed, OPS etc. It is hard to justify why Mussina's overall PB value is almost a full point less than Mays. What does all this mean really?

In terms of practical consequences, PB value effects your position in the monthly FA draft. If you are one of the 6 teams with the worst record---the team with the worst PB value gets 1st pick.
I am not sure if this applies in the season launching Draft.