here's a trick I use on secondary axis bar graphs
If I understand your problem correctly, then what you end up with is the bar from the secondary axis plotted on top of the bar for the primary axis.
If so then try the following. If you have a1:a4 for the first axis and b1:b4 for the second axis, move Col(b) to Col(d). Then select the entire area, a1:d4 and start the graph wizard.
Pick "column" as your graph type, click "finish". Now you have 4 series graphed in a bar chart but the central two series are blank. Then type the same number (I used 1) in cells c1:c4. Youll see the rightmost of your "blank" series show up on the plot. Double click it and tell it to go to a secondary axis. Then double click the 4th series (this is the one you originally wanted on a secondary axis) and tell it to go to a secondary axis. Delete the values in C1:C4. That should give you what you're looking for.
hope that helps