With Prism 6.05 and 6.0f, you can't reliably set the border color of bars superimposed on column scatter graphs.

When plotting column graphs, Prism lets you plot every point as a scatter plot but also superimpose a bar showing the mean or median and perhaps an error bar.

Maintaining the color of these bars is the problem due to a bug introduced in Prism Windows 6.05 and Mac 6.0f. Of course we'll fix this bug in the next release.

Bug details: 

Windows - If you double click on the graph to go to Format Graph, and then choose to change the border color of bars (one bar or all), everything looks fine on the graph. You'll see the colors you chose. And everything looks fine when you put the graph on a layout, or export it. But if you copy-paste the graph, or send the graph to PowerPoint or Word (using the Send button), the colors of those bars change. Moreover, if you save the file, then reopen it, the colors change. In addition, if you right-mouse click (instead of using Format Graph) on an individual bar to change the border color of that bar, you’ll see there is no color change once a color is selected. 

Mac - There is no issue when you copy-paste or send the graph to PowerPoint (using the Send To button).  The border colors of the bars remain the same.  When you save the file, then reopen it, the border color of the bars change (error bars do not). 

There are three workarounds.

Workaround 1 - Use color schemes. Don't change the colors using the Format Graph dialog. Instead apply a color scheme. Or create a color scheme to match your tastes and apply that. The colors of bars superimposed on column scatter graphs are stable when applied as part of a color scheme. When applied as a choice in the Format Graph dialog, however, the color change is temporary and will revert to the color scheme colors when you save/reopen, when you copy/paste, or when you send to PowerPoint or Word.

Workaround 2 - Make bar graph first.  First make a column bar graph, and adjust the bar colors so they are what you want. Only after setting the colors, change the graph to have it be a column scatter graph with superimposed bars. When done this way, the bar border colors won't change. 

Workaround 3 (Windows only) - Right-mouse click to format. Right-mouse click on the bar and choose Format This Bar and then click Border Color.  Note: you will notice that the border color of the bar does not change when a color is selected. But, if you save and reopen your file, you will see the border color of the bar change to the color you've selected. So, right-mouse click on the bar to format the border color of the bar, save and reopen the file to see the change.

Note that the problem is with the overall bar showing the mean or median. The error bars colors can also be set, and that works fine. 

Learn about color schemes