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<< Click to Display Table of Contents >> Navigation: MLS 2026 Fully Integrated Accounting > Payroll > Payroll Troubleshooting Guide |
Payroll is one of the most sensitive and important areas of any management system.
When payroll problems occur:
👉 they can affect:
•employee trust
•tax reporting
•accounting balances
•government compliance
•payroll liabilities
•year-end reporting
Fortunately, most payroll issues are usually caused by:
•setup errors
•missing data
•incorrect employee configuration
•outdated tax tables
•incomplete processing steps
rather than actual software failures.
This guide will help isolate and correct the most common payroll difficulties encountered within MLS 2026.
•Employee setup errors
•Incorrect pay method
•Missing timeclock data
•Incorrect commission setup
•Incorrect payroll period selected
•Missing labor entries on workorders
1.Review the employee Pay Methods setup
2.Verify workorder labor entries
3.Confirm timeclock records
4.Review overtime settings
5.Recalculate Gross Pay
6.Compare results to prior payroll periods
•Employee missing payroll period code
•Employee marked inactive
•Gross Pay not calculated
•Payroll period processed incorrectly
•Timecard missing
•No earnings generated
1.Verify employee setup
2.Confirm payroll period assignment
3.Check timeclock and workorder activity
4.Re-run Gross Pay Calculation
5.Verify deductions were processed
6.Confirm Payroll Accounting was completed
•Outdated tax tables
•Incorrect W-4 setup
•Wrong marital status
•Incorrect exemptions entered
•State formulas not updated
•Incorrect payroll frequency
1.Verify Federal tax tables
2.Verify State tax tables
3.Confirm payroll period type
4.Review employee withholding setup
5.Confirm additional withholding amounts
6.Recalculate deductions
⚠️ Do NOT simply override withholding amounts unless absolutely necessary.
Correct the underlying setup problem first.
•Payroll Accounting not completed from prior payroll
•Printer alignment issues
•Invalid bank account setup
•Missing check format selection
•Payroll checks not generated yet
1.Verify prior payroll is closed
2.Confirm payroll checks were created
3.Verify bank account setup
4.Test printer alignment on plain paper
5.Review check format settings
6.Confirm check numbering sequence
•Previous payroll still open
•Payroll Accounting not completed
•Gross Pay processing incomplete
•Payroll period conflict
1.Complete Payroll Accounting
2.Verify prior payroll closed correctly
3.Check payroll period numbering
4.Re-run payroll review procedures
⚠️ MLS 2026 will not allow overlapping payroll periods.
•Employee forgot to clock out
•Manual edits incorrect
•Wrong payroll date range
•Duplicate sessions
•Missed punches
1.Review Time Clock records
2.Edit incorrect sessions
3.Remove duplicate entries
4.Verify payroll date range
5.Recalculate Gross Pay
•Advance entered after Gross Pay processing
•Wrong employee selected
•Payroll not recalculated
•Advance not saved properly
1.Verify advance record exists
2.Confirm employee code
3.Recalculate Gross Pay
4.Review payroll deductions
•Incorrect employee accrual setup
•Manual adjustments not entered
•Incorrect hire date
•Excessive advance sick pay
1.Verify employee accrual setup
2.Review Days/Year settings
3.Confirm hire dates
4.Review prior payouts
5.Adjust balances carefully if needed
•Missing General Ledger accounts
•Invalid payroll defaults
•Incomplete accounting process
•Deleted General Ledger account
•Manual accounting edits
1.Verify Payroll G/L Defaults
2.Run General Ledger Analysis
3.Confirm all payroll liability accounts exist
4.Review payroll deduction accounts
5.Re-run payroll accounting if appropriate
•Payroll processed after year-end closing
•Incorrect payroll adjustments
•Tax tables updated mid-year incorrectly
•Employee deduction setup errors
1.Review Year-To-Date payroll totals
2.Compare Payroll Tax Reports
3.Verify quarterly summaries
4.Review employee deduction history
5.Confirm Payroll Year-End Closing timing
•Tax payments not entered
•Incorrect tax payment processing
•Manual checks issued outside payroll
•Incomplete payroll accounting
1.Run Payroll Tax Report
2.Run Zone Tax Summary
3.Review tax payment history
4.Confirm all deposits entered
5.Verify Federal and State payment setup
•Payroll Accounting not completed
•General Ledger defaults incorrect
•Payroll processed outside normal workflow
•Manual journal entries
1.Verify Payroll Accounting completed
2.Review General Ledger postings
3.Run Trial Balance
4.Compare Payroll Period Summary to G/L
5.Verify liability balances
The most common payroll problems involve:
•Outdated tax tables
•Incorrect employee setup
•Wrong payroll periods
•Missed timeclock punches
•Incorrect overtime settings
•Skipping Payroll Accounting
•Manual overrides without correcting setup
•Incomplete General Ledger defaults
•Processing payroll before reviewing reports
Before EVERY payroll:
1.Review employee setup
2.Verify timeclock records
3.Confirm tax tables are current
4.Calculate Gross Pay
5.Review payroll carefully
6.Process deductions
7.Review Net Pay totals
8.Print Payroll Period Summary
9.Print payroll checks
10.Perform Payroll Accounting
11.Backup payroll data
⚠️ Payroll should never be rushed.
Payroll errors can create:
•employee frustration
•tax penalties
•accounting problems
•government reporting issues
A careful review process is always recommended.
This troubleshooting guide works closely with:
•Payroll Processing
•Gross Pay Calculation
•Payroll Accounting
•Payroll Reports
•Payroll Tax Setup
•Employee Time Clock
•General Ledger Troubleshooting
•Payroll Year-End Closing
Together, these sections provide a complete payroll management and troubleshooting workflow within MLS 2026.