i changed my 2nd meal to:
1 Can Tuna or Chicken/Turkey Breast
1 Cup Brown Rice
and i got my fish oil tabs for my EFA's and some olive oil and almond butter in my diet.
I also have flat feet, the only thing we can do is buy inserts for our shoes so that they raise the arch. Since i bought some i havnt really had any trouble with my knees.
The cause is probably your diet, can you post an example of a workout day? and if you work you biceps out every other day you are probably overtraining which leads to muscle loss.