The first time I tested bubble columns, I made a 2x2x2 cube of water source blocks over magma blocks. One out of the 4 columns produced a bubble column. But repeating this, none seem to, even with the exact same setup. It seems bubble columns spawn only inconsistently.
EDIT After some more testing, this seems to be related to block updates. If you have a 1x1x3 column of water sources (the 3 is 3-tall in the Y axis) over a magma block, contained by glass, you'll properly get a bubble column. If, however, you break one block of glass at the bottom of the column, letting the water flow out, half the time you'll get a bubble column with no flowing water, the other half you'll get just a regular column of water with the water flowing out. And you can change between these simply by updating the magma block underneath. The expected behavior would be that, regardless of block updates, you'd have a bubble column and then flowing water out the side.
EDIT 2 After some more testing, I was able to reproduce the issue in a consistent manner. Screenshots of the process are attached. It's a 1x1x3 column of all water sources, a magma block below, and a contained 1-block outlet on the side of the bottom water source.
"Starting" shows how the column looks normally – notice it's water and not bubbles.
"First Placement" shows what happens when I click once with a water bucket on the magma block, thus placing a fresh water source at the bottom of the column. Notice the water now flows out properly, but it's still not bubbles.
"Second Placement" shows what happens when I click again in the same place with a water bucket. The bottom source turns into bubbles and it stops flowing out (you can see the outlet water starting to diminish).
"AutoReset" shows that, once the outlet water disappears completely, suddenly the column turns back into water sources and the bubbles disappear, resetting everything to the initial starting state.
I'm starting to think this has less to do with block updates, and more to do with the way the water source at the bottom interacts with water around it. Either way, now that I've found a consistent reproduction, you can build it yourself and see the odd and surely unintended behavior.