Fix my notation for lists of matrices, part 1
Jelly, 20 15 13 11 bytes

Fðs⁹œsZµḢḢL


Try it online!

Background

Like most things, this challenge is rather simple once you've figured out what you have to do. And I eventually did, after three deletions and one rollback...

First, we must figure out the dimensions of the matrices. That's easier done than said: the first element of the first element is the first row of the first output matrix, so its length is equal to the number of columns of the square output matrices.

For example, if the input is

[  [[1, 0, 0],   [[ 127,  63,   31],   [[1, 0, 0],   [[0, 0, 0],
    [0, 1, 0],    [  15,   0,  -15],    [0, 0, 1],    [0, 0, 0],
    [0, 0, 1]],   [ -31, -63, -127]],   [0, 1, 0]],   [0, 0, 0]]  ]


the first element of the first element is [1, 0, 0], whose length is ℓ = 3.

If we flatten the input and split it into chunks of that length, we get all rows of the output matrices, albeit in the wrong order. For our example input, this gives

[  [1, 0, 0], [127,  63,   31], [1, 0, 0], [0, 0, 0],
   [0, 1, 0], [ 15,  0,   -15], [0, 0, 1], [0, 0, 0],
   [0, 0, 1], [-31, -63, -127], [0, 1, 0], [0, 0, 0]  ]


To obtain the final output, we must first split the row array into ℓ chunks of equal length. For our example input, this gives

[ [[1, 0, 0], [127,  63,   31], [1, 0, 0], [0, 0, 0]],
  [[0, 1, 0], [ 15,  0,   -15], [0, 0, 1], [0, 0, 0]],
  [[0, 0, 1], [-31, -63, -127], [0, 1, 0], [0, 0, 0]] ]


Each column is now one of the output matrices, so transposing the resulting matrix of arrays is all that's left to do. For our example input, that gives

[
 [[1, 0, 0],
  [0, 1, 0],
  [0, 0, 1]],

 [[127,  63,   31],
  [ 15,   0,  -15],
  [-31, -63, -127]],

 [[1, 0, 0],
  [0, 0, 1],
  [0, 1, 0]],

 [[0, 0, 0],
  [0, 0, 0],
  [0, 0, 0]]
]


as desired.

How it works

Fðs⁹œsZµḢḢL  Monadic link. Argument: A (ragged array)


F            Monadic chain. Argument: A

F            Flatten A. This yields the vector V.


       µḢḢL  Monadic chain. Argument: A

        Ḣ    Head; retrieve the first element of A.
         Ḣ   Head; retrieve the first element of the first element of A.
          L  Compute ℓ, the length of the resulting array.


 ðs⁹œsZ      Dyadic chain. Left argument: V. Right argument: ℓ

  s⁹         Split V into chunks of length ℓ.
    œs       Split the result into ℓ chunks of equal length.
      Z      Zip/transpose the result.