Tier 1 extension application returned - invalid/old forms

Hi I am in a lot of trouble and will appreciate advice. I hired a consultant to help me with my application for tier 1 extension. We applied 5 weeks in advance but the consultant submitted the wrong fees. Home Office first acknowledged the receipt of correct fee but then 3 weeks after the expiry of my LTR returned the application to the consultant citing less fee. He never told me that the application has been returned only saying that the Home office is asking for the balance and this will not effect the outcome. 4 weeks later the Home Office returned the application directly to my home address saying that the application was invalid as it was made on old forms. Only then I realised that the consultant had kept me in the dark. I asked the Home office for advice as my leave had already expired. They said that I should stop working and immediately make a fresh application explaining these circumstances and the case worker may consider it if there is sufficient evidence that I made all possible efforts to make a valid application in time. I have done exactly what they advised. I have attached all previous acknowledgements from Home Office and my e-mails with the consultant. Now I am without a job and overstaying here while the Home 0ffice decides. I am very anxious and tense about this situation. Can any one tell me if I have a chance that my application will be considered sympathetically.

Thank you

OB

P.S. I fired the consultant and took the full refund.