I think the point being missed is this: The two masses were nearly identical and moving at the same velocities. This means that the energy or work done by the expanding gases in the barrel are virtually identical, and that the recoil energy would be the same. This is not really up for argument, since it's so obvious. If you want an equation for this, I suggest KE = 0.5mv^2, or kinetic energy is equal to one half of the square of the bullet velocity multiplied by the mass of the bullet. These numbers should come out to be pretty darn similar for the two custom loads that the OP presented to us.
The difference, as the OP has pointed out, was in the pressure of the rounds. I suggest that the higher pressure of the .40 means that the gases in this cartridge did their work more quickly than the lower-pressure gases in the .45. Essentially we're talking about F (force, or the pressure exerted) = m (mass of the bullets, which is the same) * a (acceleration, or how rapidly the bullet changes velocity). If the force is higher in one cartridge thanks to the higher pressure and the mass is the same, then the acceleration must increase to keep the equation balanced. Keep in mind that the force of the expanding gases are applied to the entire sealed system of the chamber, case, barrel, and bullet. Since the bullet moves away, the gases are going to push the case and bolt-face toward the shooter to compensate, thus recoil.
So, if we go back to our first equation, we have equal final kinetic energies but one bullet accelerates to that energy level quicker, meaning that the expanding gases are going to push toward the shooter in compensation faster or an imbalance in the system will result. This is why, even if they have the same total recoil energy, a high-pressure round like the .40 is going to have "sharper," that is really "quicker" recoil. It's not really subjective - if you put identical test barrels on a machine that graphed force over time, the 40 would have a higher peak recoil force than the .45, despite the fact that the two rounds have equal energy. However, the .45's force pulse would be longer. It has been a long time since I took calculus, but I imagine that if the energies are the same, then the integral of the force over time curves would be the same - that is, the area under the force x time curves would be equal.
If we were able to exaggerate the differences in pressure and diameter with a large-diameter projectile made of lighter material and a smaller, higher-pressure round with normal bullets, the difference in recoil speed or "snappiness" would be exaggerated still further - while the muzzle energies remained the same.
James: I think you're missing the concept referred to as "work." Yes, the velocity of the bullet and the speed of the gases under a rocket are related to moving the associated items, but the velocity is not the cause. The speed of a body has no ability to directly affect the speed of another body unless the two have actually collided, and a bullet never collides with anything in the gun - it only moves down the barrel, resulting in friction. In the example of the rocket, it is the force of the excited gas molocules pushing (creating pressure) on the inside of the rocket engines and the nozzles which accelerates the rocket and creates its velocity. In the gun, it is the force of the excited gas molocules pushing (creating pressure) on the inside of the casing, bolt face, barrel, muzzle, etc. The difference is, unlike the rocket, they are restricted. In a totally closed container, constant pressure (the force of gaseous molocules on the container) does no work (which is measured in units of energy), because to have work something must be moved. In a container like the chamber/casing/barrel system of a gun, the pressure can only do work in one direction, which is to accelerate the bullet out of the barrel. Since the force is able to perform work (that is, accelerate the bullet) in only one direction, the associated "equal and opposite reaction" must have its vector in the opposite direction. Thus, it is the pressure in the chamber rather than the speed of the bullet which is actually the agent doing the work. The presence of the bullet simply allows the system to be "temporarily closed" which results in the pressure increase. As soon as the pressure overcomes friction, the bullet begins to move and increase the volume of the closed system, meaning that the pressure decreases as it moves down the barrel. It's all precisely timed, which is why it is possible to achieve very different results with different powders - they all produce pressure at different speeds and with different curves. To achieve maximum velocity in a cartridge without exceeding the maximum pressure allowable, you have to pick a powder which will exert the most permissible pressure possible on the bullet for the longest period of time achievable - (this means keeping the force of F=ma as high as possible for as long as possible, keeping the bullet accelerating quickly) thus, the most energy imparted to the bullet, and since energy and velocity are related, the more energy the more velocity. Velocity of the bullet is not the cause of anything - it is the result of everything.
DISCLAIMER: I don't have a degree in engineering, but I did take some engineering classes, and I had a great physics professor. Take out of the above what you will, but I can assure you it is correct in essentials.
Another edit: Regarding the idea that recoil is perceived as snappy because of slide movement only, this is disregarding slide velocity. If there are two different pressures working on the slide, then slides of equal weight will have different velocities, momentums, energies, etc. Since the pressure peak of the 40 is higher and shorter than that of the 45, it is likely to accelerate more quickly and therefore reach the top speed and the slide stop faster, thus pressure is related to slide-induced felt recoil.