Consider this chart, it just shows the salary of the employees in a 3D Bar chart.

The wizard shows X Axis: Min, so lets put 500 as the value in... However running the chart again gives the same result.

The workaround is to change your chart type to 3D Column (instead of 3D Bar Chart).
Running the page gives us this result, so yes it's different, but for this chart the wizard is correct. Later you can change the chart type again and it should be ok.
So again we want the Y Axis to start with 500 instead of 0, so we define the Y Axis: Min in the Axes Settings. (see that now Y Axis: Min is listed and not X Axis: Min)


!! But there is even a nastier bug related to the above...
Let's say we kept the 3D Column chart type but added a scrollbar for the X-Axis.
Running the page shows us this! The chart is only partially visible.
This is related to the previous bug... as we defined a value of the X-Axis Min when the chart type was still 3D Bar Chart, APEX still keeps that into account... (that is why the workaround worked before). However in this case it has a negative impact on the way the chart is shown.The way to correct the issue is, change the Chart Type back to 3D Bar Chart, delete the value that is in X-Axis Min, hit the Apply Changes button, edit the chart again and change the Chart Type back to 3D Column.
Running the page again shows the correct chart.

(Found in APEX 4.0.2.00.07).