That sounds like a sled tilt issue… I assume when you say shallower at the top, you mean the top cut with respect to the bottom cut, not the top of a cut with respect to the bottom of the same cut.
I’ve noticed a little ‘wiggle’ at the start of a lot of my cuts, but if your cuts are crooked, then your initially settings are probably really far off.
If there is some bowing in the peice of plywood I noticed that my calibration cuts would vary a little in depth between the top and bottom cuts. I ended up using some screws to flatten my plywood out.
Regarding the lines not being straight. Did you chamfer or round over the edges of your sled? Or is the bottom of your sled somewhat rough? Before I smoothed out my sled, there was some ‘sticktion’ that the sled had to overcome before moving down. I think this made a similar wiggle to what @madgrizzle described.
Could it be the bit is slow to penetrate the wood? Is there some form of force beyond the z-axis lead screw helping to keep the router pressed down toward the sled?
I recalibrated last night and, due to logistics, I ended up putting my Florida 1/4-inch plywood that I use for calibration on Maslow so the bow was outward. Long story short, big mistake. After the machine cut, I went to measure distance between cuts 1 and 2 and discovered that there was no cut 2 or 5. I had 1, 3 and 4 though.
I reran and watched to see what happened and it turns out that the bow in the top right, even though clamped, was so severe that the top of the sled was tilted so far outward such that router bit never touched the plywood during cuts 2 and 5. Lesson of the day, put plywood so it bows inward and then clamp it.
Today’s lesson is not to listen to the previous lesson. As I discovered, when the 1/4-inch bowed plywood is placed so it bows inward, there’s nothing to hold the bottom edge of the plywood up since it extends out farther than the lip of the bottom beam/leg… I’d post a picture of the cut/scab that resulted from the plywood guillotining down on my ankle, but no one really wants to see it.