The Story of the Merle Cocker-Updated 2006
In October 1979, a male cocker was born in a Missouri USDA kennel
His registered name was Rusty Butch
Little did anyone know that this buff cocker who was out of mainly pet breeding for 4-5 generations would be eventually well known for the rucus he would cause 25+ years later.

Rusty was bred by a woman named Jan Whitlow. Now whether a merle something jumped the fenced and Rusty was a result, no one will probably ever know. Or possibly Rusty really was a pure bred buff cocker, and his papers were used in a merle breeding to 2 bitches both possibly owned by the same person. Or POSSIBLY Rusty was a mutation from the non merle gene to the merle gene.
Rusty was sold to E Carr.
A few years later, a person named Cleo Kent bought 2 buff bitches, one from a Missouri Kennel bred by Efton Pendergrass
who died at age 93 in 2005, the other from a breeder named David Landis.These 2 bitches were named, Penny Locks and 
Timberline's Betty.
C Kent was also a commercial breeder who sold to brokers.
One time, in March if 1988, about 8 years after Rusty was born, these 2 bitches were bred to him a week apart.. And merle cockers appeared in 1988.
Out of Penny Locks, there was Carrie's Muffin II, a merle bitch. Out of Timberline's Betty, a male merle named Rog's Snuffy was born.C Kent was also the breeder of Little Boy Blue Of Cee Kay and Blueberri Patches, among other dogs.
Both Timberline's Betty and Carries Muffin II as well as Bluberri Patches were sold to R & C Murray another kennel in Missouri.They then bred these to other dogs and produced merles and sold them locally as well as around the country.
K Crass, a Missouri USDA kennel who is still in business bred her B/W bitch to Rog's Snuffy and produced K-Jac's Fancy a merle bitch. She was bred to a buff male and produced K-Jac's Cricket, another merle bitch. She was bred to a  B/T male of her's and produced Spooky Jane a merle bitch who was born in 1997 and who is behind several merle pedigrees.
C Murray bred their merle bitch, Bluberry Patches to Little Boy Blue Of Cee Kay also a merle, bred and owned by Cleo Kent.
Prince Alex of Iron Lake, a double merle, was bred by a C Rittenhouse, and was later sold to D & A Powell and brokered by the Sparkmans. This double merle was bred to several bitches and produced many merle pups.
Most merle pedigrees still have Prince in the first few generations.Which brings us to the current merle cockers.
R Claxton another Missouri USDA breeder who has been around many years bred her B/W bitch, Iron Lake Miss Tiffany to Prince Alex of Iron Lake, a double merle, who was used/brokered by the Sparkman's Kennel who were also USDA and brokers in Missouri. 
ALL go back to Rusty Butch and 1 of these 2 bitches.

Old time commercial breeders who knew some of these people who also had gotten merles from breeding to the offspring of these 2 bitches,
From these merle breedings laying low for around 25 years, they certainly weren't in it for the money as most if not all of these breeders were USDA, sold to brokers for little or nothing.
The internet wasn't around then, so no one could advertise this "RARE color," other than in magazines and newpapers, and weren't able to attempt to make larger amounts of money like some merle breeders do now.
With the advent of the internet and the search for the unusual, some breeders started taking advantage of these RARE cockers and breeding them and selling them to others for breeding.
With the internet only being really popular and accessable to all in the past 15 or so years, it appears like these merles have appeared out of nowhere when in fact, they have actively been around for over 20+ years.

Update 8-2006
After much study on the merle issue, we have also found that Rusty Butch was bred previously in 1981. There has been no information associated with any "roans" being registered from this earlier breeding.
So one can surmise that, either something may jumped the fence and both litters of merle puppies were unknowingly registered to him...which a bit off that the same  "unknown" dog would breed 2 different females.
Or with Dr Keith Murphy's recent research on the merle gene, that possibly this gene for merle, since it is found in all dogs, may have been bred down and hidden in the buff breedings from either the 2 bitches or in Rusty. Most wouldn't have noticed the unusual merle in the buff coloring, or butterfly nose, or possible blue eye(s) to make them question what it was, and just regsitered the dog as the color it appeared..such as buff. Or as he and several other geneticists have surmised..that it was a mutation, which would happen in only 1 dog..not an entire breed or variety..
A recent hypothesis suggested that possibly since these dogs were mainly pet breedings for many generations even though they did go back to very well known show lines, that these breeders really didn't realize what they had or misregistered the dogs as far as color or pattern.
One example would be:
That Rusty Butch and /or the 2 females were both CLEAR sable merles.
If you were to breed 2 clear sable merles together, you could come up with the "blue roan" in other words, dark merle pups.
With the earlier breeding of Rusty Butch, if he were a clear merle sable himself and bred to a regular buff, the pups all could have been buff, and of course hiding any merling.

No one will probably ever know for absolute sure, but after 30+ years of this dog being born, whether purebred or opps, the offspring and the many generations are now considered pure bred.