As far as I can see, there are 2 possibilities for that.
1) Your employer has requested 09/30/2013 as the end date in the H1B petition - you may confirm this with your employer.
2) Even though 3 years is requested in the petition, USCIS might have come to a conclusion that approval is required only for 1 year. There could be various reasons for them to arrive on that decision, like the supporting documents related to the project work could not clearly state the project duration as 3 years or the need for that position in the project for 3 years, USCIS has concern whether the petitioner can pay the H1B holder for the requested duration, etc. (These reasons are just my thoughts).