@drm4610
Only customer invoice transactions that have items linked to income accounts will show on your P&L. When you say "I have checked the Item List to make sure all the information is correct but I didn't see any errors.", are you saying that all items on the invoices in question are mapped to income accounts and are still not showing under income on your P&L? Invoices with items mapped to non-income accounts will do exactly as you describe - they will show under customer transaction reports but not on your P&L. If the invoices in question contain items linked to income accounts and are not showing on your P&L it can only be a few things:
1) You may need to rebuild your data. (File > Utilities > Rebuild data)
2) Make sure the invoice date is within the P&L dates (basic, I know).
3) Make sure the invoice is paid if you're running the report on cash basis (also basic).