Are you sure they are the right size? Often boots which are too big will often also be too high over the instep an this can cause shin problems as you are not properly flexing the boot.
If you put your foot in the shell without the liner and have your toes just touching the front how much space is behind your heel. Also if you move your foot into the middle of the shell how much space is over your instep when your knee aligned.
That takes me to the last thing. What type of footbed do you have in them? Often having the foot pronate will drop the instep an again cause shin problems.
There is a boot help thread btw. Next time ask your questions there.