If you have bad or duplicate payers in a return, and the 'Add to Payer Manager' box is checked on that input form (W2, 1099's), when you rollover that return or open/close that return, those bad payers get added back.
This is why I add multiple W2's and all categories of 1099's in Customize Master Forms and click the 'add to payer mgr' box TWICE so it's unchecked by default.
The missing feature of ATX Payer Manager is the preference to have the 'add to payer mgr' checkbox off by default. Then you can check the box if you find a payer is not in your list, and you think you'll use it again. Would also be great if you could choose which forms you want to use Payer Manager with. For example, I'd only choose W2 and 1099R.
People often enter account numbers or account names (escrow, rental, etc.) after the bank name on 1099 INT and DIV which you do not want in your payer database.
But honestly, duplicates, crazy long names, incorrect EIN's, typos, etc., are not really that big of a deal, especially if you sort payers by EIN instead of name, which is the better of the two ways to use payer manager.