It is probably worth looking for a potential change in your set-up which may have caused new stresses on your body. I have been suffering with chronic knee pain for the past 18 months, and it was mainly due to increase in intensity in too short of a period. This damaged my ligaments/tendons which continue to flare up through exercise. Is there anything that you may have changed such as a new saddle, new shoes etc?
It's always worth remembering that changing items likes shoes/cleats/saddles will have a knock-on effect with your height, even if it's minuscule. Unless the saddle is exactly the same model, it may sit higher or lower than the one previous and cause discomfort when riding.
You say you have had a bike fit, although from what I have heard these can be somewhat of a personal affair (vastly-differing opinions from shop to shop). I've never had a 'professional' bike fit, but managed to find my own comfort zone by adjusting my set-up in tiny amounts to see what differences it made. It could well be that your cleats (providing you have them) are positioned incorrectly, or alternatively your saddle is too low. Try small adjustments, even such as raising your saddle 5mm at a time and seeing if this helps.
I've learnt from experience after making some changes in terms of saddle and cleat choices prior to a 1400 miles cross-Europe cycle ride for charity. I needed to get it right in time, but not rush my set-up. I cannot emphasise how important small, gradual changes are as your body needs time to adjust.