My guess is that the ages of the olive oil and the basil play a huge part in the final taste, as well as the varieties you choose. The flavor of these varies from batch to batch and variety to variety. You are probably aware that there are many varieties of basil with different degrees of pepper and sweet flavors..
There is also the issue of the age of the basil, pine nuts and olive oil. Anything that is verging on going bad, especially oil, can have some funkiness.
If you are freezing then thawing your pesto, you might end up with flavor issues, but usually not.