Income Statement simply reports the balance in the accounts within the range specified.  If you have an Expense account in the middle of the range of income accounts for your credits, then the Income Statement will be off.  You need to have all the accounts within the range be the same type of accounts.  
 
Sales Relief for credit memos needs to either post to Bad Debt in the Expense section or to an Income Account for Sales Adjustment (or whatever) in the Income section that is defined in AM-C as an income type account with normal Credit balance, then when it actually carries a debit balance it will show bracketed on the income statement and be subtracted from sales.  
 
If you have the account incorrectly defined, change the type in AM-C, then use UT-K-D to rebuild it.

How does GL-A compare to the trial balance?

The problem is the accountant and how he sees this.  I've got my head so confused with all this that I can not see straight.  The reports are correct, he does not see the closing entries as valid and sees erroneous data.  Please remove this topic.  Sorry.