I'll move your thread to the Repair area, when I get a chance.
I'd first recommend making sure all the pads are sealing properly. Our resident repair CE has mentioned that even if some pads "look" like they're sealing, that they might actually be damaged, particularly if you have low quality pads. He's got a machine he recommends testing with.
However, I'm not sure what you're referring to regarding the low C not playing in tune unless you add the low E keys. I played contra for awhile -- a Leblanc paperclip to low C -- and if you're referring to the fingering t 123|ooo | E (o = open, t = thumb F, not the octave key), that sounds more than a little odd. If you're talking about the lowest C (the Model 41 is a low C contra), it sounds to me like holding down the low E is making the pad seal better.