Depending which sidas you got, you may be able to get it custom molded and stabilized. The flash fits work very well for that. Often with a non custom you will find that your foot is not in an ideal neutral position. This can affect both the positions of your leg in the cuff but also how you flex the boot.
By the sound of it you have a little much space above your foot, which is meaning your not flexing the boot properly. This is indicated by the fact you only feel the shin at the top of the cuff.
It could help to align your foot and also possibly to raise your foot inside the boot, to try to maximize the flex of the boot.
Prob best bet is to take them back to the fitter, tell him your problems and see what he recommends, but get those footbeds molded for sure, if you can.