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I've been working on cleaning up our configuration files for quite some time now. With one AIX 6.1 machine when I copied over the new NRPE file and restarted NRPE, all of the passive checks became stale. The checks were OK for the longest time and sometimes one or two will report OK, but minutes later back to UNKNOWN.
If reverting to the previous file didn't fix it, then it's probably not the issue. Even if it did, that would be extremely weird since NRPE and NSCA don't really have anything to do with each other.
I would probably ignore NRPE if it's working correctly and try to debug NSCA. Were there any other changes to this system around the time they starting going stale? How is send_nsca set up and running on the system? Do you have passive checks coming in successfully from other hosts?
All checks were disabled and re-enabled at one point forcing the passive checks to be active checks. This triggered the stale command on a schedule. Went through each service and disabled active checks.