Taking damage on the same frame as killing a boss results in $75 being set to 4, where normally $75 is always 0. This can occasionally prevent speed values from being added to enemy projectile positions, illustrated here with the bullet-boost leaving 4-1A causing a desync (though other bullets in the level are affected too).

trace logs from frame 487 for both taking and not taking damage: http://pastebin.com/sqkrSDe7 http://pastebin.com/zFeBTbUq (I have not yet analyzed these)

edited trace logs corresponding to frames 2536-2537 in this movie, for $75=0 and $75=4: http://pastebin.com/DeW5DMMV http://pastebin.com/N1zYULW0