Payroll Net Check doesnt match amount actually paid

We upgraded from GP10 to GP2013 about 6mo ago. I installed the Year End update around 1/1/14. We run payroll weekly and every week since the update we've had the same recurring problem: the check is cut for more than the actual calculated net pay for some employees. The following are also associated with this issue:

1) The check cannot be voided (says check does not exist)

2) The check posting batch is out of balance by the amount the employee was overpaid (account affected is the Cash account bc it's paying them more than the liabilities and expenses)

3) Sometimes the Federal and/Or State Taxes are not calculated at all but other standard deductions are

4) The Recreate Check Stub feature will display correct amount but shows where the direct deposit was for the wrong amount.

5) All checks affected so far have garnishments (either court-order and/or notes/loans from our company). We use PIP for our garnishments not greenshades. It does not affect everyone with a garnishment.

6) Some of the affected employees would have netted zero & been in arrears, but not all. It only adds money to their pay never takes it.

Microsoft's suggestion to our partner was to re-sequence the deductions to: TSA deductions, Standard, then Garnishments which we tried and less people were affected but it still occurred. This is creating major issues with net wages and taxes, not too mention paying people extra, non-traceable amounts. Having it affect a handful of people a week is burdensome for us. Through testing, I think I've ruled out an issue with minimun net pay and maximum garnishment rules. The amount they're overpaid is not consistant either, I can't narrow down how it gets the number but it does vary by the deduction sequence when testing.

If anyone has any ideas, I would appreciate it. We're not getting a lot of assistance from Microsoft, they believe it's just a sequencing problem which it is however, why it's consistantly happening every week since the YE update seems questionable.

Thank you.

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