Normal soil pH, where bedrock is deep enough not to affect it much, depends on the yearly rainfall amount. Where there is sufficient rain, pH is on the acid side; and drier areas have more alkaline pH. Where the deep soil is more alkaline than the surface, one possibility is that limestone (or some other alkaline rock) below the soil layer is affecting the pH of deeper soil more than the surface soil, which depends more on rainfall amounts.
Is your climate rainy or dry?