I very much doubt there is any difference with payment method. Seating availability is based on many factors. As you have noted, status is the same for both flights, so that is not the key factor here. The expected load factor and expected passenger status mix will come into play. So for a week-day morning or evening departure that is likely to fill later with high-status members, QF will block out the front rows for those higher status members. A middle-of-the-day or weekend flight is less likely to fill late with high-status members so a Silver member may be presented more forward rows.
Exit rows on domestic flights do not appear to be blocked/reserved for high-status members, so are often available for selection by Silver members.
Another factor for seat selection can be the actual fare class paid. The exact formula used to determine seat availability is not published so we are all guessing and basing assumptions on personal experiences and what we have head on forums such as this.
As always, check again regularly and especially at T-80 and closer to the departure date as the options available to you are very likely to change.
sorry - I should have stated - ALL factors are the same! Same fare, same early morning departure, same route, same day of the week (well, Tuesday and Thursday), same aircraft (and on two of the three flights same 767 configuration, the other one is slightly different). Can choose exit rows on booking paid by credit card. Can't with the one paid by bpay!