The reason it's easier with the engine off has to do with the way a motorcycle transmission works. The gears are constantly meshed with each other, but only one set is actually locked to the shafts at a time. They slide back and forth on the shafts and lock into each other with pegs (dogs) that fit into slots on the adjacent gear. These pegs are undercut a little so that when they are engaged and under load they will not allow the gear to slide sideways. This is why you can apply shifter pressure when accelerating and the transmission will not shift until you roll off throttle.
When the clutch is fully disengaged, the load comes off the gears and they are free to slide on their shafts. If there is any tension on the gears due to a dragging clutch, the pegs will hang up and resist moving, making neutral hard to find.
likewise, if you try to shift at a standstill, you may be trying to force a peg into the side of the next gear(not the slot) which of course will not work. rolling the bike a little in either direction allows the slot to line up with the peg and it shifts easily.
2004 Rebel 250, 2003 BMW K1200GT (roadburner), 2004 BMW R1200GS(all purpose),
1973 Norton Interstate (in a box in the basement)
1968 Triumph Bonneville