Late filing of service tax returns

I had filed my OCT 14-MARCH15 service tax return on 20th April,2015

On 20th July,2015 ( on 91st day) I realised that due to error I could not pay the right service tax amount initially . So on same day I paid the balance amount with interest and generated the challan.
I tried to upload the return the same day but it refused to accept , as unfortunely it has crossed 90 days time limit.
Service tax department refused to accept the hard copy as they say they don't have such powers.
Please advise me how to proceed further
regards
n.mehta