I guess I would question the premise. Pitzer is ranked #39 (tied) currently by USNews. Scripps is #35 (tied), so not really a material difference. You could pay to see exactly what happened, but I assume it is going to be something relatively trivial.
OK, but why then are Pomona, CMC, and Harvey Mudd higher? Well, I am not willing to pay, but back in 2018 (so this is a while ago) an unlocked peer and counselor reputation spreadsheet showed them at (peer/counselor/total):
Harvey Mudd 4.4/4.6/9.0
Pomona 4.4/4.4/8.8
CMC 4.2/4.5/8.7
Scripps 3.8/4.3/8.1
Pitzer 3.7/4.2/7.9
There is enough variability in all this that I would say Pitzer and Scripps are again about the same, but then Pomona, CMC, and Harvey Mudd are in a higher tier.
Why? That is a very complicated question, but I think it is really because in their own ways Pomona, CMC, and Harvey Mudd have all distinguished themselves in certain ways that Pitzer has not. Like, per capita, Pomona is a top 10ish feeder to academicky stuff, Pitzer is not. CMC is a top 5ish feeder to businessy stuff, Pitzer is not. And Harvey Mudd is a top 5ish feeder to techy stuff, Pitzer is not.
So I think that is why Pitzer (and Scripps, about which I could say the same things) are not in the same reputational tier as Pomona, CMC, and Harvey Mudd. It is not that Scripps and Pitzer did something wrong per se, but it is very competitive to get a lot higher reputationally. And Pomona, CMC, and Harvey Mudd have each been able to compete for those higher reputations, in their own individual ways.