It's in your store configuration in the section below:
Attachment 59141
Though there used to be a foreground and background colour choice for both the main and secondary colours. Seems that there is only a choice of three of those now. Just shows how out of touch i am with the workings of eBid nowadays. I've no idea when that change was made.
If eBid are now forcing both background colours to be the same that could be what has screwed up your store; it was probably ok before they did that.