When you create upwards bubble columns they tend to cancel out around the ones next to them or walls. Usually, when there is a three by three soul sand (or more) space, the middle one cancels out, but when walls are put around them the bubbles only are on in a diagonal pattern. Walls also by themselves cancel out them too. This doesn't affect downwards bubble columns (magma blocks).
This is intended. At least one horizontal neighbor must be a pure water block (source).