I've modified it like this:

Select dt1.Cuenta,dt1.Descarga,Sum(Balance) From (Select A.Cuenta,A.Descripcion,
Isnull((Select Balance From CNTBal03 Where Cuenta=A.Cuenta And Periodo=12 and Fiscal='2003' ),0)
+Isnull((Select Sum(Debito-Credito) From CNTDET02 Where Cuenta=A.Cuenta And Periodo=1 And Fiscal='2004'),0)+
Isnull((Select Sum(Debito-Credito) From CNTDET02 Where Cuenta IN (Select Cuenta From CNTCuentas Where Descarga=A.Cuenta) And Periodo=1 And Fiscal='2004'),0)
 As Balance, A.Descarga From cntcuentas A) dt1
Group by dt1.cuenta,dt1.descarga
Order By rTrim(lTrim(dt1.Cuenta))

But I'm still having problems at the top levels, the totals are ok in the lower level but the upper levels are still getting wrong results.

For example in the following tree

Account        Parent
1              
10             1
100            10
100-01         100
100-02         100
100-03         100
100-04         100
100-04-01      100-04
100-04-02      100-04
100-04-03      100-04

The totals for all sub accounts are correct but the totals for account 1,10 and 100 are incorrect. Anyway I think I'm closer now.