Power Supply Design w/Transformer - Not Enough Current
As the value of the rectified DC input to your buck regulator stays the same @ 39V, it's unlikely that the transformer is at fault.
You wish to draw 12V @ 50mA from the regulated output, i.e. 0.6W.
A transformer rating of 1.8VA is more than adequate.
I calculated the ripple voltage on the storage cap and likewise get a 3.8V drop during the diode non-conduction period,
Something else is amiss.