Accounting Question, Please

[MJ]

I am in the process of finishing my 2006 tax return which I do annually with TurboTax. I was hoping I can get an answer to my question.
In 04/2006, I sold my 2 family house where I lived and rented out the 1st floor apartment. In 09/2004, I put in a new roof which I began depreciating 1/2 the cost. I was surprised that Turbo Tax based on the 2004 date did not add 1/2 of the left over roof cost to the business portion of the cost basis. Is there something I need to do to capture the bulk of 1/2 the cost or am I out of luck. According to TT, if I had installed the roof 7 months later, I would have saved nice a $1k.

Any help pointing me in the right direction, besides suggesting a good accountant, would be appreciated.

Thanks

MJ