When doing FMQing, I know I tend to tense my leg muscles too ... go at it for a constant stretch, whereas when piecing, you do a seam, stop and relax. Then do another seam etc, So I understand what you are meaning.
Yes definitely ... think of the ergonomics and how it is effecting your body and what you can do to alleviate. How high is your chair? Moving your foot pedal back closer to your chair might help. Also, is your machine set into a table? or on top of a table? These are a few of the things that I would consider.
By chance does your machine have a stop/start feature where you do not have to use the foot pedal?
That might help a lot if it's primarily your ankle and leg that is being affected.