Not sure why the peak frequency would drop like that but did you try raising your enclosure tuning to fix this issue?
If you made a bigger box for the 4 12 setup, it should had displaced more airspace in your listening env. This should have raised your resonant freq.
To me a Yukon's peak frequency is probably right around 43-45 hz...so yeah if you're peaking at 40, it won't be optimal for all out SPL...