I connected my Sony DAT recorder by an optical cable to one of my Envy24
cards. Mudita24 has got a tab called "Hardware Settings" with an option
named "Master Clock".
"Master Clock" has to be set to "S/PDIF In". I don't see this option for
alsamixer. Your S/PDIFs are routed correctly, you don't need to reboot
or to start jack.
S/PDIF input does show incoming audio signal here, after switching to
"S/PDIF In" for "Master Clock".
Google is ready to search for "envy24 alsamixer master clock" ;).