Was your bike fit static or dynamic?
If it was static, get a dynamic one done, it may pick up something in your pedal stroke.
What’s your core strength like? Do you do any core specific exercises? The legs can do funny things without a stable platform to work from.
How old are you? Around 40 people often start to reveal niggles from misalignments that they’ve carried all their lives but youth has been compensating/masking for them.
Numb toes, are your shoes too tight?
In short, I don’t think it’s anything to do with the chainstays. Assuming your wheel runs in the centre of the frame, measure crank to wheel to put your mind at rest.