Here are some possible reasons you could be out of Balance: 

Balance Forwards

When going live on the system you load balance forward.  The subject and eligible amounts should always be the same unless the deduction or liability has a limit and it has met the limit.

Correct:

Incorrect:

Wrong/Different Basis Codes

Each deduction and liability is set up with basis codes.  You will find all the earnings codes that the deduction or liability should calculate on as well as pre-tax deductions that will reduce the subject/eligible amounts.  We see in the example below that the basis codes are different for the FICA Deduction and FICA Liability.  This causes the subject/eligible and amounts to be different.

Wrong rate/limit

The user maintains rates and limits and must update them as needed.  A rate or limit could be incorrect on a single deduction or liability causing the PR Employee Accumulations to be incorrect or in the case of FICA shown below the rate could in wrong on the liability and not the deduction. 

Posted to wrong state

If the timecard has the wrong tax, unemployment, or insurance state the accumulations may not be correct.  This can be corrected by doing a negative timecard with the original date to the wrong timecard and a positive timecard line with the original date to the correct state.  See link for correcting timecards Here

Payrolls are not closed or do have the final update flags checked

Once the payroll is closed, you need to run the ledger update one additional time.  The audit lists may have 0.00 amounts but posting the batch will flip the final flags.  This ensures that all the sub-ledgers have been updated and allows the sub-ledgers to be closed in GL Month End Close.