I'm not an expert...but it sounds like you have FAH setup to run as a service, so it starts on system start-up. When you launch the console manually you are running it a second time. If you only have one FAH program and folder, you are working on the same WU twice, at about half speed. I can't imagine this is a good thing.
If you run the console as a service you don't have to (shouldn't) launch the progarm manually. To check the status of the program, look at the FAHlog file or UnitInfo file. The log file contains all of the text you usually see in the console window.
I will start a new thread shortly, once I update the ping list