The material in the
equation environment simply doesn't fit in a single row, so
amsmath is forced to place the equation number one row lower.
To keep the display-math material from exceeding the column width, you'll have to introduce a line break somewhere. The following screenshot provides two possible solutions (the horizontal lines are there just to illustrate the width of the columns):
V_S(x)=V_1 \Theta(x/a) + iV_2 \delta(x/a),\\
V_S(x)=V_1 \Theta(x/a) + iV_2 \delta(x/a)