Christian, If it helps, I was able to isolate my problems down to a specific catalyst; syntax errors in my exclusion lists.
Based on some of my testing I attempted to add new entries to RegistryExclusion.exl. capture-server would report "Errors in RegistryExclusion.exl" and the result would be the conditions described in my earlier post. Another secondary result was that the capture client app would crash/fail on occasion. I selected the "Send Report" option so you may have received that information yesterday. I'll send a general post to the group on the proper syntax I should be using. Thanks.
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