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I've got this blend file (got it from here). So the mystery is that the origin point's color is cyan. Checked the options in theme colors, "Active Object" entry is set to orange (as it expected) and when I change it, it only changes the outline color of the object. Newly created objects have their origin point colors orange and the "Active Object" entry controls an outline color and an origin point color but not for the objects that were already in the scene.

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Objects that are used in multiple scenes will have their object origins displayed as cyan.

The file that you linked to contains 2 scenes, 'bottom' and 'side', as shown in the 3D header:

enter image description here

The object 'body' for example has a blue origin because it is used in both scenes. This means if you move the object in one scene the position of the same object in the other scene will also update to match it. You can see how many scenes an object is being used in by looking on the 'Object' panel of the object and noting the number of 'users'. In the case of 'body' it is being used in 2 scenes:

enter image description here

You can separate the object in one scene from the other by clicking the '2'. Instead of one object linked between two scenes you would now end up with two independent objects, which are no longer linked.

Also see 'Copying and linking objects between scenes' and 'Linking to a scene' in the Blender Wiki Manual.

If the outline of the object and the object origin were blue it would be because the file was linked from another file.

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