Look through the nagios.log file. It might tell you something. Check your file permissions. Especially in var.
It almost sounds like when the system is booted, nagios is reading an old cache file (that hasn't changed for many days due to bad permissions).
Nobody should be using the beta versions of nagios, unless you like to troubleshoot or have a particular dire need for it. If after you have become an expert with nagios v1.2, then yea, have fun and troubleshoot.
My suggestion is to move to the stable v1.2 and leave the debugging to the beta tester's. We are production users, and need to have something working NOW, not tommorrow.