However the union is subsequently apparently happy with the World Cup squad with one leader saying it was "more representative" than ever since apartheid was officially dismantled two decades ago.
Meyer revealed his 31-man squad late last week. It included nine players of colour which gets it very close to the required threshold.
Those players are Bryan Habana, Zane Kirchner, Siya Kolisi, Tendai Mtawarira, Lwazi Mvovo, Trevor Nyankane, Rudy Paige, JP Pietersen and Damian de Allende. Yet even there things are messy.
The Zimbabwe born and raised "Beast" Mtawarira faced questions over his eligibility even after his first Springboks selection in 2008, because only South African nationals can represent the country in sport. The granting of citizenship appeared to end the debate in 2010, but there are now claims that he should not be included as one of the players satisfying the quota.
Mtawarira has said: "I am a South African at heart. I love this country. It has become my home. It is everything to me."
But in a country with a cruel history that has left enormous scars and problems, this is not always enough.
There were also questions over whether de Allende - a rising star alongside centre partner Jesse Kriel - is of colour. Only in South Africa might you find words like these: "He (de Allende) is also a valuable commodity in the South African context in that he is a player of colour with parents of mixed descent."
In this unfortunate situation it is impossible not to pull up a picture of de Allende and judge whether he looks like a player of colour. But apartheid has taken many prisoners, and still does so.
South Africa's past was one of black and white horrors producing many shades of grey. In stereotypical terms, the Boer community was seen as the most hardline proponents of apartheid, a system only officially introduced in 1948 by the National Party. In simple terms this "legalised" attitudes and rules that had existed anyway. Apartheid's segregation kept the minority white community in control of the power and wealth and reduced the black and coloured people and later Asians to prisoners and slaves.
Rules and practices of this horrid "apartness" can be traced back to the Dutch colonisers and miners of the 1700s, and white English settlers were portrayed as more moderate apartheid beneficiaries, if moderate is the right word.
And yet the Nobel Prize-winning author Doris Lessing wrote that there were blacks and coloureds who preferred - again if that is the right word - the more blatant racism of the Boers, compared to the duplicity of the English position. Complexities, everywhere.
Repairing a broken country has proved extremely difficult. Lingering racism may well be working against black and coloured rugby players, and yet the rapid fire promotion of those players might not help the cause either. Rugby quotas began in 1999 and were reintroduced last year when the South African Rugby Union said seven players in each Springboks match-day squad of 23 would be non-white, and at least two of those must be black from the beginning of this year.
SARU CEO Jurie Roux said: "It's not just about numbers on the field. We understand that it is unfair to put that pressure on the Springbok coach without offering him any assistance - his teams can only reflect what is going on at the elite end of the domestic game."
Roux said massive transformation had taken place, that 84 per cent of under-18 players were black Africans. But Meyer' recall of veteran white players like Victor Matfield has helped fuel suspicion about the coach's strategies.
Sports Minister Sikile Mbalula used his Twitter account to urge South Africans to be patient with the pace of transformation in rugby.
"We need a winning team that is black and white going to the World Cup," he said.
Habana, one of the greatest wings in history, gave his full support to the coach.
"This is unfortunately something that is always going to be a part of South African rugby," Habana said.
"I'm fully behind Heyneke's standing in the situation and wanting to make this World Cup a successful one for South Africa."
Presuming the Springboks do get to play, the question now is how the furore and race rules impact Meyer and the campaign.
During the two-test series against the Pumas, Meyer was quoted saying skin colour had no impact on his selections.
"I don't look at colour, I look at the best players," he said.
"I'm totally committed to transformation and I have a great relationship with my players."
In this one, short incongruous quote, Meyer highlighted the confusing situation, and even added to it.
