Most likely from improperly prepared base problems, but could be from poor quality mix, cold mix, poor compaction, and high ambiant temperatures and heavy traffic. Maybe a combination of all these things. I've also seen a lot of pavement laid from ten-wheeler end dumps that segregated in the dump bed and in the laydown machine, particularly in the augers. This almost always results in a poor surface condition within a year or two with a lot of larger or course material lying together without much fines in it as a binder. This almost always happens in the loaded portion of the pavement, though I've also seen it clear to the outside.
On the poor quality mix, many times this comes from the first load or two from a batch plant in the morning, or an oil-rich condition, which also is common first thing in the morning.
Something else to consider is base temperature, plus rain or snow sometimes. All will occasionally cause surface problems that don't always show up right away.
Another problem cause is a base surface that hasn't been properly compacted, or one that has a high sand content. The sand tends to migrate under load and given time, will cause surface problems. Then too, I've seen asphaly pavement laid on top of chipseal, which then migrated under heavy loads and high tempertures.
In California, where you are, and in other places too, heavy traffic is sometimes released on top of new laid blacktop too soon before the surface has time to cool off properly. Pavement subject to this stress will compress further unevenly.
If I had all night, I could probably think of a dozen more reasons.
Just thought of another reason. The use of Clarco's will also cause segration of the mix. Frankly, the more a mix is moved around, the more segrated it will become. Clarco's are mostly used with belly dumps, so the bad protions are a bit further apart than with the hauling done by end-dumps.