If my net Schedule C income is around $10,000, why does Turbo Tax say I can contribute $9,000 to my sep ira? I thought the limit was 25%.

This suggests that you mistakenly told TurboTax to calculate the maximum 401(k) contribution.  Either delete the Keogh, SEP and SIMPLE Contribution Worksheet and then re-mark the SEP Maximize box or tell TurboTax that you made an individual 401(k) contribution and unmark the Maximize box for an individual 401(k).

Thanks!  This fixed the problem.  I just clicked on "Maximize" in the wrong place!