Yeah it does. If nearly all your payments are via credit card, the credit card payment is just shifting the balance from "regular" AP to "credit card" AP. So the GL impact of those is a GL Credit to Credit Card Payable right? That's an increase in the payable balance so it shows as positive on a search. If you pay with cash, the credit to cash is a decrease in that account balance, hence it's negative.
It's not really explained that well that saved searches use natural accounting balances in the Amount field. So it's not always necessarily the case that a positive=debit and negative=credit. That might make more sense if you add the Amount (Credit) field to your search. I'm betting that both the credit card and cash payments will have an entry in that field, even though one is positive and one is negative in the Amount field.