The "already running in batchmode" message means that one of the application's processes is still running when you or the operating system tries to launch it again. Open your operating system's process manager (Windows Task Manager, Mac Activity Monitor, etc.) and look for one or more processes named SpiderOakONE or SpiderOakGroups. End those processes, and after waiting a moment to make sure they do not reappear, launch the application again. That should get you going again.
If you keep the task manager open, you should see two SpiderOak processes start up as you launch the application. One is for the GUI, and the other for the backend, so it is normal to see two when the graphical interface is running.
If the problem recurs, you may need to double check any antivirus, firewall, or other security software and in them whitelist SpiderOak One or Groups. Some security software mistakes SpiderOak for a threat and may try to halt its processes, which could be the root cause for this difficulty. If it was just a one-time thing, chances are the application simply didn't cleanly shut down the last time you used it.