The error is due to the well-known R gotcha that the : (seq operator) takes lower precedence than arithmetic.
So a[i-3:i] doesn't do what you want it to do a[(i-3):i], it does a[i - (3:i)]). So the medians you are printing are of:
4-3:1 # i.e. 1:3
8-3:1 # i.e. 5:7
12-3:1 # i.e. 9:11
16-4:1 # i.e. 13:15
SOLUTION: always parenthesize arguments to : if they involve arithmetic or are expressions: a[(i-3):i]