Debbie,

'True' color plaster pools always have a much greater chance of having issues than a traditional white plaster pool, hence the waiver. On a color plaster pool, were they add a dye to to give it color is more likely to have shade variations, mottling (dark grey areas), and check cracking. However if you are going for a color look, there are alternatives that are less likely to develop those symptoms. Such as an exposed aggregate finish.
Just be sure that whatever surface you choose, always follow their startup procedures, such as brushing the pool frequently when its a new pool, and keeping the water chemistry balanced for a new pool. This should reduce the chances of these problems happening.

Here is a link that might be useful: Pool Service