If I understand correctly what you were saying, the "incoming transaction" notification shows up when a transaction is broadcasted on the network (and is waiting confirmation).
Because it's been some time you didn't sync that wallet, the first time it knows about those old transactions is when the block is updated but it's all there already.
After that client is fully in sync, check if notifications come up again when you get a new payment.
But I usually never leave it opened, like I said I open it once in a month or so, and it always showed the notifications even if they are old. Some are recent tho, like 2 days ago but didn't show up. I'll see what happens next time. Because it's been some time you didn't sync that wallet, the first time it knows about those old transactions is when the block is updated but it's all there already.
After that client is fully in sync, check if notifications come up again when you get a new payment.
