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I have recently had to reinstall FMS9 and updated OSX Leopard Server to 10.5.8 and am having these problems (It was working fine in 10.5.7). The WPE works just fine mostly but does stop on occasion. I managed to get rid of the red bullet which prevented me from editing the Web Publishing settings at all, and now it is just black... but works but still sends the errors.
Does killing the fmservicewrapper work for v9 too?
HOW do you kill the fmservicewrapper? Terminal presumably but what am I looking to do there?
in your case, I would not kill it. My case was different, because both DB server and WPE were set to not start automatically after reboot of the server.
See rather this long thread, maybe you get some hint there: