I don't know if there is a proven scientific basis for it or not but many people complain about polycarbonate lens.
It is not a 1.6 lens but in lieu of a 1.6 lens. It is cheaper cost wise and more impact resistant but some complain of distortion with it especially higher myopes.
If your old lens aren't poly and the new ones are, then that might very well be your issue.
With all the consolidation in the optical industry, most businesses, including your "independent" optician push whatever lens they make or have a coop agreement for. Most of the lens sold as high-index aren't, they are poly or a proprietary material.
If you want a brand name lens such as Hoya or Zeiss and true 1.6 or higher, you must says so everytime you buy lens.
Seems highly unusual for material to have such a profound effect. I'm assuming the headaches are secondary to the vision being unclear with the new glasses. Do the old glasses still give you good vision? Other causes could be poor fit of the glasses or alignment of the bifocal component (although it does not sound like bifocals) or a change in prescription in which case you should get a new refraction from your optometrist/ophthalmologist if it's been 3 years.