There are actually multiple issues here, at least:
WalletView::processNewTransaction only looks at the first of a batch of inserted rows.
QSystemTrayIcon's X11 implementation (QBalloonTip, internal-only) only allows a single notification, destroying the previous when a new one is shown
- Showing possibly hundreds of notifications would be terrible UX
It seems like the GUI should queue notifications at the same "instant" (eg, a new block), and if there's multiple send a summary of them all (number of transactions, total sent, total received/mined). This may require some refactoring work, as notifications currently follow the TransactionTableModel insertion slots.