What version of Ledger are you running? 6.8A or 6.8B or 8.0A? This matters.

After running Close Year, you are correct in clearing the posting journal (for the posted batch to retained earnings) and the batch status report. At this point, the balances for all Income Statements should be zero. If not, there are two usual reasons:

1) You ran Close Year for a range of departments but not for all of them. Some accounts/departments have not been processed by Close Year.
2) You have posted another batch and updated the totals of at least one Income Statement account.

If either situation is the case, then you need to re-run Close Year to deal with the remaining accounts.

You might also want to check data integrity.