Another is scrunching up a towel with your toes
Your knees could be a running technique issue where it is not going away with the work you are doing and you think it would return if you stopped doing it.
When jumping rope and running are your heels kissing the ground?
Are you landing ball of foot or on your toes?
When running or jumping rope you may be using different muscles than you have in the past.
If you increased time jumping rope or distance/time running too quickly that could be an impacting factor.
Have you noticed any improvements?