Cody explained it pretty well, but I want to just add an example. Traits that are influenced by several loci come out more from line breeding because you are using less diversity, thus increasing your chances of producing the same traits in the babies as the sire and dam. When adding in new animals, you add in new genes and reduce the chances of being able to predict offspring phenotypes.
On a simpler scale, it's similar to eye coloration and skin pigmentation in humans... there is a sliding scale where all genes from one side of the spectrum will produce a lot of pigmentation (as in dark brown eyes and all dominant genes) and the other side of the spectrum will remove (not produce) eye pigmentation (as in light blue/gray eyes and all recessive genes). Polygenic traits work like this sliding scale, but I believe GTPs (and others) have several pigment traits which is why you can get a green with also a lot of black spots.