Blocks disappearing

Ever since 1.4.6 came out I've had blocks disappearing from my mineshaft, it's the same spot every time, it's not endermen either. It's a huge hole down to the mineshaft with a track system (on top of wood planks) to the top, at the very beginning where the rail system starts are where the blocks are disappearing

]]]]]]][[[[[[[[]]]]]]]]]]]]]]]]]]]]]]]
]]]]]]]][[[[[[]]]]]]]]]]]]]]]]]][[]]]]
]]]][[]]11111111111111111111^^^^
]]][[]]]11111111111111111111^^^^
]]][[]]]11111111111111111111^^^^
]][[]]]]11111111111111111111^^^^
]][[]]]]11111111111111111111^^^^
]][[]]]]11111111111111111111^^^^
]]][[]]]11111111111111111111^^^^
]]][[]]]11111111111111111111^^^^
]][[]]]]11111111111111111111^^^^
]][[]]]]11111111111ppppppppp^^^^
]]]]][[[[[[[[[]]]]]]]]]]]]]]]]]]]]]]]]
]]]]]]][[[[]]]]][[[[[]]]]]]]]]]]]]]]]]
(It's perfectly square all the way around, just hard to get it pictured using letters/characters lol)
] = Railway
p = plank
^ = where it starts to descend
1 = blank space

It's 2 plank wide all the way around (rail on the plank on the inside, fencing on the plank on the outside), with the p being extra planks with fencing on top surrounding the button hub to start the track

Everything in the p section is disappearing, the plank with the button, fencing, rails, but it's only in this 1 area, no other blocks are disappearing anywhere on the track or anywhere on my map/around my base