Origin 8.5 is an early version, and we could not fix the problem in it. But you also can try the following workaround.
If you want the columns with error bar in two layer using double Y Axis. You can: 1) Make sure your input data is designed as X Y1 Yerror1 Y2 Yerror2 (five columns).
3) But in step 5, instead of check the Column/Bar Gap/Offset Across Layers check box, you should go to the Spacing tabs for each plot and change the spacing to 70%(or other values according to your need). Click "OK"
4) Go back to the graph, select layer 2 (click on the 2 icon in the top-left of the graph).
5) Move it to the left either by dragging the mouse or using arrow keys. You may refer to this graph to see the effect when layer 2 is selected, and also how the graph will look like.