Couple important things to remember...
Inbreeding can't create genetic problems, it merely strengthens existing genetic traits.
Simple recessive genes are actually the easy ones to understand... there are other genetic traits which are quantitative. The outcome in any given pairing is somewhat unpredictible but certain traits become stronger as they are reintroduced. Everyone knows how this applies to positive traits, if you want really yellow leopard geckos you find the two brightest yellow animals you can find and breed them... then breed the brightest offspring, then breed the brightest offspring, then breed the brightest offspring, then... And so on. This can be applied to negative traits as well.
Many morphs are the result of a recessive trait. Since the recessive trait is most easily replicated by crossing animals known to share the trait, line breeding is common.
IF an individual used in the initial breeding project (to prove out the trait or begin commercial production) has a genetic tendency of any kind, that tendency will eventually come to the surface, even if hidden. Most of these clearly genetic tendencies towards negative deformities were likely introduced early on, via a carrier animal which displayed no outward signs of the problems. The earlier in the program it was introduced, the more widespread the problem is.
A breeder should be very careful not to breed any kinkies that he or she feels are genetic, they should be removed from any breeding program and sold as pet only IMO
Is a sentiment I fully agree with, although I take it a step further. Nobody can guarantee beyond a shadow of a doubt that any animal they produce will never be used in a breeding project unless they have it sterilized (not gonna happen, herp surgery is expensive enough as it is). Humane euthanization is a very valuable tool when it comes to keeping not only your own projects, but the general captive population safe from genetic defects. Culling any offspring which display a negative trait which can't be verified to be formative or due to injury is good for the animals and good for the hobby... If you have adult breeders which regularly throw offspring showing a deformity, they should also be removed from the breeding population. If you have siblings of deformed individuals, same scenario... Any clutchmates of a deformed individual are carrying the same genes which caused the problems for the kinked animals.