Hey Robert,
Yeah the order of installation can make a difference. A key factor when setting up Sitworks for the first time is to point it to the proper data folder. This is done on the path screen after a complete system reconstruction, or alternatively if you delete the AllSites.xml file from your C:\Trimble Synchronizer Data\<Controller Name>\Trimble SCS900 Data that can also be used to reset the file path.
Note that the <controller name> defaults to PC when you first run Siteworks, so if you already had a folder of data on the controller, or synced one down to the controller using Office Sync you would want to point the Siteworks path to that location.
Hopefully you got yourself sorted out. Let me know if you have any more questions or can't get things working. But basically if you have a folder with all your data on it on the controller, you can delete the AllSites.xml and then the next time you start Siteworks, point it to the folder location.