So its recent article on the Karmapa makes for some interesting reading. If the article has any credibility there may be more to this inter-sect rivalry, and, according to them, some basis for suspecting PRC involvement in these things.
The Kagyu sect - also known as the Black Hat sect by virtue of the magical headgear woven of goddess hair worn by the Karmapa on ceremonial occasions - disputes the presumption of the Dalai Lama to speak on its behalf. Kagyu adherents point out that the Karmapa holds precedence as a reincarnation over the Dalai Lama since the Karmapa reincarnation was initiated over 100 years before the first Dalai Lama was enthroned. The seat of the Karmapa was the Tsurpha monastery inside the present-day PRC; the 16th Karmapa fled to Sikkim with the Kagyu sect's most important regalia and treasures, and established an imposing new seat called Rumtek a few miles outside the Sikkimese capital of Gangtok.
This institutional friction was exacerbated in the 1960s when the Dalai Lama's decidedly un-Buddhist brother, Gyalo Thondup - who was the US Central Intelligence Agency liaison for the secret war against the Chinese occupation of Tibet - spearheaded the creation of a "united front" that would centralize the control of the fractious emigre community and sects under the control of the government in exile in Dharmsala. The other sects were apparently loathe to bow to Gelugpa control and formed their own political organization, the "Fourteen Settlements" group under the leadership of Gungthang Tsultrim.
In 1977, Gungthang was assassinated. His assassin allegedly told police that he had been paid $35,000 to commit the crime by the government-in-exile, and further alleged that he had been promised a bounty of double that amount to kill the current Karmapa. 
Efforts to centralize control of the emigre community collapsed, leaving a residue of bad feeling between Gelugpa and Kagyu leaders.
The situation was complicated by a split within the Kagyu sect itself upon the death of the 16th Karmapa in 1981.The conflict boils down to the rivalry between two Rinpoche in the Kagyu order, Tai Situ Rinpoche and Shamar Rinpoche ("Rinpoche" is an honorific typically applied to reincarnated lamas).
They have battled for decades over control of Rumtek and its ecclesiastical and worldly treasures (which are now in legal limbo; Indian courts have awarded control to a trust established by Shamar Rinpoche, but the local government has not taking the politically traumatic step of evicting the partisans of Tai Situ Rinpoche, who actually occupy the facility).
They also continue to battle over the very identity of the 17th Karmapa.
Tai Situ Rinpoche claimed to have found a secret note from the 16th Karmapa that directed him to the boy subsequently acknowledged by the Dalai Lama and enthroned in 1992 as Ogyen Trinley Dorje, the 17th Karmapa.
Shamar Rinpoche had none of that, asserting that a dream led him to a different Karmapa, one Trinley Thaye Dorje, whom he quietly brought to India from the PRC and enthroned in 1994.
Adherents of Shamar Rinpoche consider Ogyen Trinley Dorje's acknowledgement by the Dalai Lama as a piece of low, Gelugpa skullduggery. An America student of Shamar Rinpoche, Erik Curren, wrote a book on the Karmapa controversy titled "Buddha's Not Smiling". Talking to Asia Times, Mr Curren characterized the elevation of Ogyen Trinley Dorje as a virtual coup d'etat against the Kagyu sect by the Dalai Lama, with the intention of elevating an easily-manipulated son of nomads to the position of Karmapa.
And not only that...
If you sit back and think about all of this for a few moments, the existence of these charges and counter charges should not be surprising. It comes from mixing religion and politics. It arises also (read more in the article) that there are local geopolitical ramifications between a rapprochement of the Tibetan Buddhist community inside and outside Tibet/China that go beyond Tibet/China; namely, into India itself.
The most useful accusation against Ogyen Trinley Dorje - one that attracted the close and hostile attention of the Indian security apparatus-is that his patron, Tai Situ Rinpoche, is colluding with the PRC to extend Chinese influence into India's Himalayan border regions...
A 1998 suit filed by a follower of Shamar Rinpoche further accused Tai Situ Rinpoche-and the Dalai Lama and his brother-of scheming to seize Rumtek, destabilize Sikkim, and hand it over to the Chinese. 
Certainly, beyond pleasant Buddhist platitudes concerning universal brotherhood, Tai Situ Rinpoche has made no secret of his efforts to re-establish his position inside Tibet with the help of the Chinese government.
He has rebuilt his traditional seat, Palpung Monastery, in western Sichuan province. His lavish website offers gorgeous views of the monastery and states that 300 students and 50 monks reside there.
For its part, the Chinese government appears to encourage the establishment of Tibetan organizations overseas that are affiliated with partisans of Tai Situ Rinpoche and promote Ogyen Trinley Dorje as the Karmapa.
In India, Tai Situ Rinpoche's reception has been less friendly. The Indian government banned him from entry into India from 1994 to1998 (he travels under a Bhutanese passport). His travel to the Himalayan border regions is restricted to Himachal Pradesh, where the Tibetan government in exile is located, and where his main facility inside India, Palpung Sherabling, is located. He cannot travel to the Northeast, Jammu/Kashmir, or Sikkim, where Rumtek is located. 
I've not written much about this thing except to say something like, "I really don't know what's going on but you have to expect countries to expect things of people living within them, and there are laws to follow." To which I'd add: And you can't expect the countries to not act like geopolitical entities, especially when they're big geopolitical entities who appear to each other to be in a zero sum game. And, to the Western Buddhist blogosphere: Don't presume automatically anything about anything here. To non-partisan parties here it is strange that the moment some outside agency raises some critique of these folks, it's always "Those Bad Non-Tibetans!" kind of response. This is especially true given that China and India have been historical enemies forever. That's why I maintain that judgment by those who aren't intimately familiar with the situation (and I for one am not) is premature to say the least.
I don't have an axe to grind in this at all, except to say that I've really liked Western followers of the Karmapa I've met in the Portland area. I hope they all work it out. And I'm sure that there are those who will respond that all I'm doing is regurgitating PRC propaganda or some such hoo-hah. But stuff happens behind closed doors.