Greek Oregano Infection

I have a problem with my greek oregano planted in sandy soil 2 years ago. There is a horrible odor to the late season pickings. Also I noticed some brown discoloration of the leaves. The pH at this site is low. We have had a cool, wet summer and fall. I hope you will have some thoughts about this.
I am thinking that perhaps I will have to move the plants to a different site or start again with new seed at a new site.

The most probable cause for your problem is a lack of sun and heat. The plants are native to Greece and therefore do best in hot sunny conditions. Such conditions are also rarely acid in pH and adding some lime to the soil around your plant could help it produce the proper oils and withstand the leaf infection better. If the smell comes from the brown leaves, it could be due to the infectous agent transforming the natural oil into something stinky! Trim off all infected leaves and burn them- just as a precaution.
Once frost has hit the plant, the smell may be off as well, because the damage would disrupt oil production and then who knows what is produced!
Another wrinkle: seed-grown plants are not identical. Have you checked that there is not some rogue plant amongst your mix of seedlings that has the peculiarity of producing a strange smell under less than optimal conditions? If the rest of the plants are OK, then it would be merely a matter of discarding that particular plant.