- PayPal includes all Sales and Shipping Income they've processed on your behalf. GoDaddy Bookkeeping includes the Sales and Shipping Income but also includes Returns
- You may have categorized some transactions as "Personal income" on the GoDaddy Bookkeeping side. Since these transactions don't affect your overall Profit & Loss, they're not included in the total displayed in your bookkeeping account. If these transactions were payments for products / services, they likely should be re-categorized as Sales (or something that rolls up to Sales and Gross Receipts).
- If you entered transactions in GoDaddy Bookkeeping manually or via CSV to represent PayPal data, that data will not be reflected in these numbers.
- GoDaddy Bookkeeping might be missing some PayPal data due to account inactivity, unforeseen problems or bugs
Since PayPal sent a copy of your 1099-K to the IRS you're responsible for reporting AT LEAST that much income on your taxes. If the number reported by PayPal truly is incorrect, you'll need to work with them directly to get a corrected copy of the form submitted to the IRS.