We recommend clearing a stompboxes system settings after updating, b/c we've seen weird problems caused by updating.  To do this, turn the Space off and then on again while pressing the right footswitch and the preset selector encoder.  After you do this, you'll need to reprogram the aux switch map.

If you're still having trouble, could you try putting your Space in performance mode by long pressing the right footswitch, and then assign the aux switch that you have currently assigned to the Bypass function to the 'Left Footswitch (aka Active Footswitch)' instead.  I upgrade a Space and went through the aux switch assignment process.  This should do what you want.