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Yesterday in trying to help another customer with some issues I discovered my NRPE server wasn't working. I fiddled with the config and such and couldn't get it working proper. I ended up uninstalling, rebooting, verifying that the configs and modules were all cleared out of c:\program files\nsclient++\* and then I did a clean reinstall. Things just worked.
Is that a possibility here?
You might want to grab a backup of nclient.ini and your scripts directory before doing it, but this is the exact situation I had just yesterday.