Either on automatic run on launch or from Since Last Run, an update of scheduled transactions will not refresh open register windows with the transactions from the scheduled transactions collection. Closing the affected register and reopening the register (without quitting gnucash) resolves the problem.

So, if I have my checking account register open, and run Scheduled Transactions>Since Last Run..., and accept the pending transactions (including a known transaction that will end up in the checking account), the checking account register will not display the new transaction until either restarting gnucash, or less invasively, close and reopen the checking account register tab.