In "doc6300 - AT91SAM9 LCD Controller", it says:

The AT91SAM9 LCD Controller is based on Blue-Green-Red (BGR) standard while most graphical layers use RGB color map.

......

Most graphical layers use RGB 5-6-5

This leads to a swap between blue and red components. There are two solutions to correct, via software or via hardware.

I see neither hardware swap in AT91SAM9261EK schematic or software swap in Timesys Linuxlink distro source. How comes the color diplay looks correct on the LCD?

The driver provides the struct fb_var_screeninfo to user-level applications. In there, the r,g,b color bit offsets and lengths in pixel data are specified. The application is then responcible to craft image data accordingly.
Currently, the driver specifies 5-5-5 colorspace(because a lot LCD's out there are 555+I, not 565 type), but that can be patched easily if hw is wired differently.
Actually, there is quite a bit of difference on 5-5-5 and 5-5-5-I on images, where gradient color surfaces are used. But handling this extra I(intansity) bit is left to the user application. Usually calculating this extra bit is not worth it, because of the calculation overhead, though.