This is a common problem when printing on any surface in nearly any media. It is called background inversion. One solution is to do the same thing that is done when screen printing a light color ink on a dark object to decrease background inversion.Heads up on those clear "waterslide" transfers, while they do in fact work great, unless you've a light color surface - you'll not be able to see it at all & if the paint on the bike isn't white, it'll drastically change the appearance/colors in the transfer. http://motorbicycling.com/f26/gas-tank-decals-23613.html
When you do your design make it in a layered format (each color separated into its own layer) and begin by printing the problem colors by first printing a white base coat beneath them and then apply the color layer in 2 or more reprintings allowing each to dry well before reprinting the individual layers.
If you practice this technique you can achieve true color transfer for almost any color of background.