Hi,
Could you try to set Cubase as Master (just for testing). In the Preferences > MIDI > MIDI Filter, make sure all options are disabled (so nothing is filtered out, even SysEx is not filtered out). Add a MIDI Track, make sure the input is set to All MIDI Ins, or Focusrite. Hit record in Cubase, and press Start on your Boss Looper. Stop your Boss Looper and check the data, you have recorded.
Are there expected Start and Stop SysEx MIDI Messages recorded in the track?