Hi Charles,
Can you please confirm: is this the first time you're attempting to publish content from this data store?
> the issue (other than it just won't publish with a generic error) is the Analyze window in service editor says the data/folder is not registered and will have to copy, but when I try to register it says it's already registered with the server.
Before trying to publish again, can you completely delete/remove the data store that is defined in ArcGIS Server Manager.
Then in ArcMap, after you perform the 'analyze' operation before you publish the map, go to the Prepare dialog window, right-click the warning and open the Register data source with server dialog - then redefine the data store here. Then attempt to publish the map.
> Rather than giving ESRI links can you tell me exactly what to do to properly 'define' the data stores in arc server?
I doubt that I can provide steps that are more detailed than the help documentation. But this also depends on where your source data is stored. It sounds like you have the feature layer in an enterprise geodatabase (aka. ArcSDE geodatabase) because you mention SQL Server. In which case, you would define a database data store. Specific steps are here:
Register your data with ArcGIS Server using Manager—Documentation | ArcGIS for Server
(under the register a database section)
In a typical workflow, you would define the database data store first, then attempt to publish the feature layer.
> What can I check to verify that it is defined properly?
After you've defined the data store, you can click the Validate button on the Data Store page in ArcGIS Server Manager. If a green checkmark appears, then you're all set. If not, then something is not right.
Hope this helps,