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Assuming you paid in 2007 California income taxes for 2004.
That is correct that amount paid was included on the schedule A - as you deduct state income tax based on the year in which they were actually paid. Be sure to report only actual taxes - not penalties or interest you might paid for being late.
As you filled form 540 - http://www.ftb.ca.gov/forms/07_forms/07_540.pdf
you should not include that amount neither in line 36 California income tax withheld nor in the line 37 2007 CA estimated tax and other payments - you should only include withholdings and payments for 2007, but that payment was for different year.
However - that amount should be include in line 39 of the form 540CA - http://www.ftb.ca.gov/forms/07_forms/07_540ca.pdf because it was included in your federal itemized deductions.