Excel do what you want,
The problem is that it tries to do what he think is right not what you want
I usually do a plot by selecting the data and adding an (X,Y) scatter graph, and usually excel doesn't get the right X,Y.
Then with the right mouse button I click on the graph and then click on "select data", here you can delete or add "Series" and tell what data is the X and what is the Y in the "Series" by selecting the data on the workbook window.
To change scale to logarithmic click on the axis you want to change the scale.
I hope I'm helping you.