I know that there quite a few posts about notification issues, but I have not found any that cover this exact issue. It seems that every time I try to change anything in the setup for Vera (I am running firmware 979), the notifications stop working for hours. Then, after some number of hours, I will start getting them again. Has anyone else noticed this?
Same here…speciafically from SChlage - no notification at all 
Mine have just stopped working. Period. A few changes and it died. Can’t seem to get the to work at all.
same here, not only do notices sometimes hiccup after I make changes but also simple scenes (such as light timers) which generally work very reliably will sometimes not work properly after recent changes (as in 24 hours or so not changes in the last few minutes) one such I’ve had more than once is a lamp timer which will activate but not turn off the first day after changes, notices seem more mysterious (knock on wood!) mostly mine have been quick and reliable, but occasionally while I am making changes to experiment with how some new scene will respond I may get erratic performance from alerts, usually though they work as advertised for me