Well I've been doing some sleuthing...I have Light Flow installed and was having some minor issues with some other notifications so I decided to uninstall Light Flow completely. After doing so I tested message notifications with Smart Alert on and they worked again. For me, I have AOD, so basically even if the message came through when the phone was on, as long as I wasn't in the messaging app it would result in a notification (icon at the top of the screen). If the phone screen turned off and went to the AOD, upon picking it up I get the Smart Alert.
So once I realized Smart Alert worked fine without Light Flow in the equation (so I knew it wasn't the phone needing a full reset or anything) I installed Light Flow again. I tried to reinstall my back up settings and ended up with problems again, so uninstalled Light Flow again and this time I installed and just set it back up from scratch. Now I have Smart Alert and all my notifications are working as I expect them to with my various settings in Light Flow. I'm sure all my tinkering in Light Flow mucked something up.
Basically I'm back in business.
ETA except apparently it isn't working with missed calls