I came to the same basic conclusion as you did EM. So having an excuse to look at some Canal itineraries, I looked at three cruise lines and their fares. I tried comparing partials with partial and full transits of approximately the same number of days. Also I just looked at itineraries, not the number of times that itinerary was offered. Some of the itineraries were a once a season as shifting to or from Alaska and many of the itineraries were offered several times during the Canal "season." With all that in mind here is my completely unscientific, highly opinionated conclusion.π
The cruise line I found that had the biggest difference in fares was Princess. A full transit of the original locks on the Island Princess was $1200. While the fare on ships using the new locks came in at right around $1000. There were many more full transits available on the ships that needed to use the new locks and only one full transit on a ship using the original locks. Perhaps a little supply and demand coming into play??
I also looked at NCL and Carnival. On these two lines there was less of a difference between cruises that used the original locks and those that needed to transit the new locks. The only trend I could easily spot was the original locks tended to run a little more, nothing huge, usually less than a $100pp.
It used to be fairly simple to determine what the toll would be for any given ship at either of the locks. The original locks was $138 per passenger berth and $148 per passenger berth at the new locks. Now that they have returned to calculating the toll based on Panama Canal Tons it is less straight forward. In any event the price per PC Ton is higher at the new locks.
One other thing that crossed my mind, is perhaps StevenUS is looking at fares on ships that have cabins for singles. I now some of the larger, newer ships that would use the new locks do have some single cabins that are not burdened with the dreaded single supplement. Maybe that is skewing fares higher at the original locks for him??