Check out the possibility of water erosion.
Many times the aggregate for cover and bedding is a single sized material with open void spaces
This forms an easy path for water to flow in the trench, after backfilling. It can cause erosion of fines, via that flow system. The place the fines came from settles.
I have seen this mainly recently after construction, since soon the voids get filled and other stable conditions develop. Pumping from the trenches as the job goes along can induce this flow also. In rare cases, artesian flow intercepted by the work can do it also.
For now, I'd examine the pumping practice, since that may be the culprit. It may be necessary to use something other than sump pumping.
In some areas the pumping from open trenches loosens the soil below the trench and so the weight of the backfill compresses that soil and the pipe settles along with it. In these cases the subsoil is usually more granular types than a clay. These situations are difficult to detect, since the excavator takes it down to grade, including "lifted' soil.
If the shale has had the weight of the earth on it before the trench work, there should be no added settlement due to the trench and the backfill, unless some subsoil disturbance is caused by the work.
If the subsoil below the pipe is disturbed and is therefore "compressible", a cradle won't help.
Those members here with experience with expanding shales may have some help.