I thought they are required to follow these and where there is a disagreement between the SC and the OC, the OC view prevails ?
Have a look at Section 232(2) of the Act. It provides grounds for seeking order for demanding the scheme fulfils its duties. If you have already attempted mediation, you can proceed to NCAT.
And yes, the SC is required to follow the instruction of the OC. Also, in this case, I suspect the scheme is required to fix the windows then, if need be, establish later who is responsible for the cost.