Hi Kevin,
The rows you are seeing in the analysis results window are possibly due to having the "Feature Access" capability enabled. Have you tried disabling "Feature Access" under the "Capabilities" category and then reanalyzing to see if that clears up these errors / warnings?
Also, I am surprised that "Mapping" is not among your list of service capabilities. It should always be enabled/available for Map Services.
Can you describe in more detail the process you're using to publish your service?
You mentioned using a service definition file. Is that still the case or do you have a map document (MXD) available that you could use for the publishing?