Hello Mark,
Another reason for the pitch excursions may be that by lowering flaps will generate various pitching moments. If you set flaps to half, the wing normally experiences a large increase in lift and a comparatively small increase in drag. Even so the center of pressure moves forward when lowering the flaps, this increase in lift creates a pitch down moment. When Lowering the flaps to full, lift is still somewhat increased, but now the drag increase is much larger. Apparently, these relationships hold true for most wings.
Now, in the Hornet, the flaps/ flaperons seem to make up a sizeable portion of the wing, so I guess that when they're lowered fully that the drag increase is tremendous. So, the decrease in speed isn't much of a surprise. Since the flaps seem to be quite low on the airframe, I also suspect that the added drag is effective below the aircrafts center of gravity, thus adding another nose-down moment.
However, there's another element to consider, which isn't rooted in aerodynamics, but in the flight model of the DCS F-18: It is said that in the low-speed range, the drag experienced by the Hornet is much, much larger than it is in the real thing, thus requiring the large throttle movements- which in turn can create their own pitching moments again. If the thrustline is, e.g. over the center of gravity, an increase in power will result in a nose-down moment. As far as I can see, the developers are also looking into the flight model, so perhaps we see an improvement soon.
In any case, I feel for you, the Hornet's behaviour in the slow flight regime used to (and actually still does) bewilder me as well. At times I have to go to almost full military power, just short of the afterburner, to control the descent rate when turning from downwind to base. This will happen even at low weights and still makes me at times scratching my head.
I hope that these explanations help you.
Happy virtual landings,
Cepheus