The amount of water soaked up by a new pond depends a lot on the type of dirt comprising the basin and the amount of thick or deep layer compaction of the basin or liner. The minimal recommended compacted clay layer as a liner is usually 2 ft thick. In dug ponds in my area with good well compacted clay for a liner that is usually 8 ft wide/thick, there is basically no immediate visible water loss once the pond is filled. The pond is filled and stays basically full until evaporation causes water loss. The looser the composition of bottom soil in a pond the more water absorption that will occur especially if there is some sort of leak through loose or improperly compacted soil. Basically all dirt bottom ponds leak, the difference is the degree of leakage from minimal to measurable loss per day.
Once you get rains with a decent amount of watershed runoff especially over frozen ground the pond will fill. Once full and input spring water becomes "normal" you will get a good idea of the amount of seepage through the basin. Then when the water level stabilizes, this gives you a good idea of how well the banks above the water level were-are compacted/sealed. Usually somewhere above the stabilized water level are the leakage areas.
You explain "The berm was built about 12" at a time and then compacted with an excavator and dozer. After all completed we rolled it in with the big loader I have talked about but we really didn't do anything to the side we were removing the dirt from." If your pond fills then recedes to near the current depth you have major leakage/s somewhere in the walls above the water level and the first place I would explore or fix is the side that was not layered and compacted.
IMO 12" thick lifts are too thick to get good soil compaction. A dozer or excavator are poor soil compactors due to the weight of the machine is spread out over a wide area. A dozer operator who built ponds told me that you can cover a chicken egg with 3" of dirt and dive over it with a dozer and not break the egg. Drive over the same egg with a bicycle and you will break the egg all due to weight distribution - wide vs narrow.
If I understand you correctly the final compaction of the soil especially in the dug out area of the basin was performed mainly on the finished pond basin by driving around with the 30ton machine. If this is correct, from my experience I would expect leaks to occur in the banks due to poor deep soil and or thick-wide layer compaction. As Esshup mentioned best liner compaction is done by building up thin 4"-6" thick layers and driving over each layer a several times with a good soil compaction machine. Best overall soil compaction machine is a vibratory sheepsfoot roller, 2nd best is a double barrel sheepsfoot roller, 3rd best is a single barrel sheepsfoot roller. The benefit of the sheepsfoot roller is the layers are knitted together to minimize water from seeping between compacted layers or layered "sheets". In good, proper moisture clay a loaded pan will do a pretty good job of compacting thin layers of clay. Digging out soil and then just surface compacting the finished dug out area results in poor deep, thick, layer compaction that is needed to produce minimal water seepage through a pond basin. When ever a just compacted surface layer dries out due to drought or animal digging the crack/hole provides a pathway for water seepage.
