I think you have your RandomTickSpeed high?
It is pretty annoying and probably not intended, but I'm guessing the game calculates when you're walking against a block and executes the jump action, and when the jump action happens twice you fly, so it's not that much of a 'bug' but more an unintended feature.
Thanks, tested it out and for me it happens whenever the ender chest is just in the first slot, when you're holding it in your second, and when it's in your inventory.
Very old bug, no need to worry.
I heard someone had this whenever there was an NoGravity tag being run on the rod. Maybe search for a command block that gives entities NoGravity? Since I don't have this problem at all.
I don't think that's a bug. I'm pretty sure you could never do that. They should add that though