I keep a 'Tips' database and here is my entry for your issue. I've used this frequently and it works.
"You probably moved some vertices around, so that the shape is not aligned with its pivot point anymore.
For example, if you draw a circle in the Front viewport, select its vertices and rotate them so they lie on the XY plane, then extrude the shape, you get the same problem.
One way to fix it is to draw a line in a viewport that is perpendicular to the axis along which you want to extrude, attach your original shape to it, then delete the line at the spline sub-object level. Now if you apply the Extrude modifier, everything should be back to normal."
Rob Holmes
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