Pretty sure I checked them both - I was very careful about locking down what not to reset in the block. A lot of the above was Al confirming what I had discovered back in June and reported to him then - he has been great.FracTool has separate items for Bypass and Bypass Mode ("bp mode"). It sounds like you didn't select the bp mode item (unchecked by default) when resetting.
Bypass = bypass state, block engaged or bypassed
Bypass mode = block behavior when bypassed, thru or mute