Renewing the sanctions, which were first imposed by former President Bill Clinton's administration in November 1997, was hardly the appropriate welcome for the Sudanese First Vice-President, whom Washington regards as an ally, even if it does not like the government of which he is now a member.
Kiir, who succeeded former Sudan People's Liberation Army (SPLA) leader Colonel John Garang as the leader of the South, is the main partner in the Comprehensive Peace Agreement (CPA) in which the US played a key role. He went to Washington precisely to lobby for lifting the sanctions and to seek more support for the budding peace process.
The US administration justified the renewal of sanctions by citing that Sudan poses "an unusual and extraordinary threat to the national security and foreign policy of the United States".
This sounds like an exaggeration, but it is well known that the US remains highly concerned about the lack of progress in the peace efforts in Darfur. The last round of the African Union-sponsored peace talks on Darfur ended in the Nigerian capital, Abuja, last October with little to show for more than a month of discussions.
The parties announced agreements on respect for human rights and on guidelines for power-sharing. But there was nothing new in these principles which have already been incorporated in the CPA.
The discussions were held back on account of demands by Darfur rebels to renegotiate the power-sharing deal agreed in the CPA and enshrined in the transitional constitution.
It was a difficult request, given that the CPA enjoys strong international support and is seen as crucial for stability in Sudan and the region. The Darfur rebels' demands include a larger share in power, and they would like a radical rearrangement of the power-sharing agreement outlined in the CPA. This would have removed the special status granted to the South in the agreement, and threaten the whole agreement.
There are still many fairly thorny issues that need to be resolved.
The other major problem is the infighting between and within the two main rebel groups, the Sudan Liberation Movement (SLM) and the Justice and Equality Movement (JEM). The SLM conducted attacks against JEM's positions earlier this year, and has since splintered into warring factions. Rebels were also accused of the kidnapping and killing of aid workers and African Union (AU) peacekeepers.
The AU deplored the continued infighting and called on the rebels to sort out their differences. There is little sign of this, as a conference convened in rebel-held areas last October failed to bring together the main protagonists, SLM chairman Abdul-Wahid Nur, and the movement's secretary-general and field commander Minni Arko Minawi.
Nur declined to join the meeting, which is seen as an attempt by Minawi to remove his competitors and take over the leadership. The splits have occurred along tribal and clan lines, creating worries that Darfur was facing a "Somalisation" threat.
The faction led by Minawi boycotted the last round of talks in Abuja, and attempted to disrupt the negotiations by breaking the ceasefire and attacking a government-held town, to the indignation of AU observers and other international actors.
UN officials have recently complained that insecurity in Darfur is hindering food and relief aid and forcing a stream of displaced people in refugee camps which are already struggling to cope with tens of thousands of refugees. The insecurity was ascribed to banditry and partly to pro-government militias. But a large share of the blame was put on the rebels.
The US has recently joined the long list of those expressing impatience with the rebels and their endemic factionalism. US officials did not hesitate to issue a strong condemnation last month of rebel attacks on AU peacekeepers. Five Nigerian peacekeepers were killed, and the SLA military wing (Minawi's faction) was blamed for the incident.
Unless the international community comes in with some strong support urgently, the prospects look pretty grim.
Press reports say that the US now considers the rebels part of the problem, and US officials have been distancing themselves from the movements. One US official was quoted as saying that the administration has no sympathy for the rebels and did not approve their programme.
However, the US still blames the government for the crisis, and the extension of the ban reflects US displeasure with Khartoum. It is also in part a gesture towards powerful groups in the US who still mistrust the Sudanese government.
The government faces another problem, the threat of prosecution of top officials accused of war crimes before the International Criminal Court. A visit by the United Nations' special rapporteur for human rights in Sudan, Dr Sima Samar, in October reminded officials of the issue by urging Khartoum to cooperate with the ICC, a request that was flatly rejected by Sudanese officials.
The US and other international actors face a serious dilemma in Sudan. International engagement is crucial for the success of the laboriously negotiated CPA which has ended the 21-year old war in the South. Donors meeting in Oslo earlier this year have pledged more than $4.5 billion for reconstruction efforts, mainly in war affected areas.
However, very little of what has been pledged was actually given, and most donors have made the delivery of support conditional on resolving the conflict in Darfur.
But if the conflict was to drag on, lack of support for the CPA may cause the agreement to unravel. This is too great a risk to take. This is the dilemma which Kiir must be trying to discuss with his hosts in Washington, in the hope of disentangling the two conflicts and leading the international engagement and support for the agreement before it is too late.
Darfur is the biggest stumbling block facing the CPA, but it is not the only one. The two major northern parties (the Umma led by former prime minister Sadiq al-Mahdi, and the Democratic Unionist party led by Muhammad Othman al-Mirghani) have refused to join the transitional government and continue to criticise the agreement as partial and far from comprehensive.
The US still blames the government for the crisis, and the extension of the ban reflects US displeasure with Khartoum.
Other important political parties, such as the Sudanese Communist parties and Dr Hassan Turabi's Popular National Congress, have also boycotted the process.
Turabi, Sudan's former strongman in the current regime of President Omar Hassan al-Bashir, has been recently released from prison and is currently touring Arab countries.
Turabi, who lost a power struggle with al-Bashir in 1998 and has been in and out of prison ever since, issued a number of warnings to the effect that the CPA is not going to achieve its objectives.
The agreement also leaves a number of issues unresolved, deferring contentious matters to later discussions, committees or elections and referendums. It took the two sides nine months to agree a cabinet and a parliament.
There are still many fairly thorny issues that need to be resolved, and the two parties have sharp disagreements over them. It is doubtful whether the process could withstand a combination of a lack of international engagement, even aggressive hostility, and the protracted Darfur crisis, a lack of support among major Northern political parties and the mistrust between the two major partners.
The next few months are going to be crucial. And, unless the international community comes in with some strong support urgently, the prospects look pretty grim.
Dr Abdelwahab El-Affendi is a Senior Research Fellow and Coordinator of the Islam and Democracy Programme at the Centre for the Study for Democracy, University of Westminster, London.
The opinions expressed here are the author's and do not necessarily reflect the editorial position or have the endorsement of Aljazeera.