Mitch
Compound bows, especially the bows of the last 10 years, is comparable to the pollution systems on vehicle.

A simple problem is often exasperated by the many possible causes or combination of causes. [:@] Go with the basics and work up.
Personally, I would check the following four possibilities first.
1. Nock height
2. Cam/wheel rollover timing (in accordance with factory specs).
Up and down flight can be the action of a shaft trying to recover from the affect of a tail high or tail low release; related to the nocking point height and/or wheel/cam timing (rollover).
3. Draw-weight vs. shaft spine.
If you are using a release, the sideways movement of an under/overspined arrow bend can often become an up and down movement of the shaft tail. I am suspicious that your shafts were close to " redlining" and that you may be slightly over-spined at this time.
I would first make sure the timing of rollover of cams/wheels and nocking height are correct, and Then I would, in small increments, add and subtract some draw-weight to see if the " dipping" stops.
4. Rest tension.
If none of the above recommendations seem to stop the " dipping," and your rest has a tension adjustment, I would add and subtract a click or two of stiffer/softer tension to the rest to determine if rest tension is causing the problem. If the tension of your rest is too soft, the vane(s) may be making contact with the shelf of your riser.