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The Super League war was supposed to be the final battleground - where issues were thrashed out so they would never surface again.
A decade later, those same problems are materialising. A new war is brewing.
Sydney, the game's traditional home is again under threat and frustrations bubble to the surface beyond the city where rugby league is generally in good health.
In the mid-1990s efforts were made to rationalise the number of Sydney teams because they were not viable. This resulted in an acrimonious split that was finally repaired with the creation of the NRL in 1998.
Just last week NRL chief executive David Gallop said Sydney clubs needed to consider merging or face extinction but many stubbornly refuse to heed the warnings despite haemorrhaging money and an uncertain future.
Instead, Sydney clubs prefer to blame the NSW state government and its 40 per cent poker machine tax for their predicament. The tax, along with smoking bans, have resulted in a 10 per cent decrease in revenue for NRL-aligned leagues clubs and the money men have found the numbers don't add up.
St George Illawarra face up to a $2 million cut in funding this year and more next, while Parramatta, Penrith and the Roosters are all facing significant shortfalls.
"We are working with the leagues club industry to provide clear projections but the message is coming through in no uncertain terms that some Sydney NRL clubs will die if things don't change," Gallop said.
The squeeze has even meant the Dragons, who recently signed Brisbane coach Wayne Bennett from 2009, have admitted they probably won't reach their $4 million salary cap. One of the best things about the NRL is the evenness created by the salary cap but this could be in jeopardy if more clubs can't afford to spend up to the limit.
Parramatta boss Denis Fitzgerald has even suggested the salary cap be reduced to $3.5 million over the next five years to take pressure off clubs.
This was met with derision from Australian and Roosters second-rower Willie Mason - never shy of saying what he thinks - who said Fitzgerald's suggestion was "the stupidest thing I've ever heard".
It's probably not, but Mason's point is valid. Reducing the salary cap will only play into the hands of the UK Super League and rugby union, who can entice players to their greener pastures.
The real answer, many believe, lies in reducing the number of NRL teams, particularly in Sydney where clubs are contesting for an increasingly competitive sports dollar.
Gold Coast coach John Cartwright has suggested a 12-team competition, with Sydney divided into four zones. Others support this and also advocated a return to a truly national competition to tap into a wider audience, reviving moves into Adelaide and Perth.
Instead of reducing the salary cap, there are increasing calls for it to increase significantly in order to retain the likes of Sonny Bill Williams and Mark Gasnier, who are both mulling over big-money moves to rugby union.
"Something needs to be done to keep our best players in Australia," Storm, Queensland and Australian captain Cameron Smith told Sydney's Sun Herald. "You don't see too many rugby union players or Super League players coming to the NRL. It just isn't worth it to them financially."
Andrew Johns agreed. "I'd hate to think in 10 years' time we are nothing more than a feeder competition for Super League or rugby union," he wrote in the Daily Telegraph.
Effectively the Sydney clubs are keeping the lid on salaries because they can't afford increases.
They are also inhibiting growth and exposure because most won't entertain merging or relocating. Tradition runs deep.
The NRL have already waved an $8 million carrot under Sydney clubs' noses in return for permanently relocating to the Central Coast, about 90 minutes north of Sydney.
It might not be long before one bites. In the past fortnight the Sea Eagles and Rabbitohs have both taken home games to Bluetongue Stadium and Souths plan to take games to Adelaide and Perth next season.
"We would love to have a team on the Central Coast," Gallop said. "It was a tough call between the Gold Coast and Central Coast [in 2005], but strategically it's proven to be the right move to go to the Gold Coast first."
The Gold Coast have been an example of the success rugby league often enjoys outside of Sydney. They attract good crowds of 22,000 at their purpose-built stadium in Robina, which was funded by the Queensland Government. Their side are also sitting on top of the NRL table.
Crowds average about 14,000 in Sydney. It's one of the main reasons the Bulldogs, Eels and Rabbitohs all call ANZ Stadium home, while the Dragons and Roosters play a mixture there and at their traditional venues.
With a capacity of 83,500, ANZ Stadium is a massive venue and rarely beyond one-quarter full but clubs are paid to play there and it is modern and comfortable.
It has been a difficult sell to many fans who would rather see their team playing in their area but the pure financials make it difficult for clubs to ignore.
Rugby league is not the only sport under pressure. The AFL is also going through a fair amount of navel gazing brought about, in large part, by the rise and rise of football while rugby union wrestles with expansion plans and ways to combat the lure and money of playing in Europe.
Qualification for the 2006 football World Cup and the success of the eight-team A-League, which the Wellington Phoenix are part of, has brought football into Australia's awareness and this will only accelerate if the Socceroos qualify for the 2010 World Cup.
Rugby league certainly has some major issues in a time when it should be celebrating 100 years.