This is the same problem I've been having since a few firmware updates ago. I reported this way back on October 10th, no replies to my thread. In the old firmware, you used to be able to hit stop on the master MIDI device, and the slaved BSP would stop. Now, as of 1.2.0.6 or later, stop message from an external master MIDI device only 'pauses' the BSP. It continues sending clock via the external clock port. This drives me insane in a live situation, as half my rig is sequenced from the BSP and it doesn't stop on command. This is a HUGE bug IMO and needs to be addressed.
Do note that if BSP is the master (sync = INT), everything works as it should. It's only when Sync = MIDI that this problem occurs.
"Stop on the DAW -> BSP in Pause
Play on the DAW -> BSP will re start from the beginning"
^ This does not happen with the External clock jack when BSP is slaved!!! Clocks keep going to the external clock Jack when BSP is 'paused'. Fail.
Arturia needs to address this.
EDIT: From my testing, I think what's happening is that the BSP is leaving the run/stop DIN SYNC pin high, when the BSP is 'paused'. The 'clock' pin stops sending clocks. This means that it's impossible to reset any gear synced via the external clock back to 1, when the BSP is the slave, without hitting the stop button on the BSP itself. This is a departure from firmware 1.1.1.6 and below. In the older firmwares, any external 'pause' or 'stop' messages were interpreted to the external clock jack as the run/stop pin going LOW. Essentially resetting back to 1, no matter a pause or a stop. This means that in the older firmwares, you couldn't do a 'pause and continue' with the external jack. On new firmwares, you can't do a 'stop and reset back to 1' solely from a MIDI master other than the BSP.
Since there's only a tip, ring, and a sleeve for the external jack, there is no possibility for true 'pause' or 'stop' messages in this case, as the external clock's run/stop pin is either high or low. It would be my personal preference to forego the 'pause and continue' function and instead, any stoppage of the BSP's clock would result in a full stop (run/stop pin low) on the external clock jack. I see how some could want this the other way, so maybe a toggle in the MIDI CC would be an option.