James,
The point sizes in v10 adjust with the number of points. As the point quantity increases the point size decreases. The font size for "B" is 10 which is the default font size, so "A" and "B" are identical in size. v9 produces the same result except the font family is Times.
Below are a few solutions you can try:
Module[{d3},
d3 = {{1, 2, 3, 5, 8}, {2, 3, 6, 9, 10}, {4, 5, 7, 10, 12}};
ListPlot[d3,
PlotMarkers -> {{"", 20}, {"", 15}, {"", 10}}]]
Module[{d3},
d3 = {{1, 2, 3, 5, 8}, {2, 3, 6, 9, 10}, {4, 5, 7, 10, 12}};
ListPlot[d3,
PlotMarkers -> {Style["A", 10], Style["B", 8], Style["C", 6]}]]
Module[{d3},
d3 = {{1, 2, 3, 5, 8}, {2, 3, 6, 9, 10}, {4, 5, 7, 10, 12}};
ListPlot[d3, PlotTheme -> "PlotMarkers"]]
Module[{d3},
d3 = {{1, 2, 3, 5, 8}, {2, 3, 6, 9, 10}, {4, 5, 7, 10, 12}};
ListPlot[d3, PlotTheme -> "Classic"]]
The last example using PlotTheme->"Classic" will display v9 default markers.
Tim