To answer your original question of why FS rounds and PB rounds vary so much in FPS when the gun remains the same, I'd first look to bore fit.
Now, I know that the SR-1 relies on the shell as a sort of ball sizer but, what's the state of the barrel beyond the shell?
LAPCO, before they released the rifled barrel, they recommended the .690 barrel for users only shooting FS rounds, and the .686 for those shooting FS and regular paint.
In the .690 barrel, regular paint (most of it anyways) in this barrel is in an overbored state so, it will allow air to blow by, reducing it's velocity (and efficiency). FS rounds on the other hand, because they will be in an effective 'bore match' state (even though they are a few thousandths smaller) and, they have that nice cup at the back for catching the air column, will come out as much as 20FPS faster.
In the .686 barrel, regular paint is either bore matched or, still overbored (but not as much) so it will be a little more efficient (and higher velocity than the other barrel). FS rounds on the other hand will be in an underbored state and because they don't compress to the I.D. of the bore as much as a regular ball, they experience a lot more friction as they move down the barrel, effectively reducing their speed to be closer to the regular paint.