One of the necessary steps for FTBBeyond (and many other FTB packages) is the FTBInstall.sh script, which must be executed as the same user as your webui login.
Older versions of the webui require you to do this manually, via command prompt.
More recent versions (say, if you update right now) include a new button in the Server Status page called FTBInstall.sh, which will download the requisite vanilla server jar.
If you update your webui, (and be sure to restart the webui service), this button will appear for you, making obsolete the need to run any scripts from SSH manually.
Note, this button does not have any indicator that it is doing anything–it creates a separate background process which (in the case of FTB) simply downloads a ~10MB file. You can check the progress in an existing terminal session or just wait a minute before attempting to start the server.