I too have this issue. It happens with both 3.0.3 and 3.0.4. I have nsca running as a daemon (it dies every couple mins and I restart it with cron), PNP, and ndo2db running.
It's very weird. After a restart, all checks are run once, then never again even though scheduled. My server receives most data from passive checks and it does received them, I can see it in the log. If you look at status detail, last update is recent, but last check is way off.
I've been trying to figure this out for a couple weeks now. No headway.