Sean,

A few thoughts... Looking strictly at the wings, deploying flaps will almost always result in a nose-down pitching moment. This means that deploying the flaps trims the aircraft for a lower angle of attack. On the other hand, deploying the flaps is likely to increase the wing's maximum lift coefficient. A bigger maximum lift coefficient means that you can probably fly slower before stalling. The trick is to retrim for the desired angle of attack once the flaps come down. Unless you get it just right, you will probably experience transients in both pitch and flight path.

As you have discovered, not all airplanes pitch down with flap extension (even if their wings experience a nose-down pitching moment). The reason is that deflecting the flaps may have a big effect on the flow over the tail surfaces. A substantial increase in downwash over the tail will cause a nose-up moment that may dominate the nose-down moment experienced by the wings. As montague points out, the effect is often exaggerated with a short-coupled tail. In contrast, aircraft with T-tails will almost always experience a pitch-down because flow over the tail is less affected by the flap deflection.

Many airplanes automatically retrim when the flaps come down (the T-38 will experience an almost uncontrollable pitch-up if the interconnect between the flaps and stabilator fails). It sounds like you are already doing it manually, but if you have the ability to couple some nose-up elevator trim to flap extension, I think you should be able to slow the landing speed down. Hope this helps.