This is exactly the problem. We have entrusted Musharraf with the responsibility of being our point man in South Asia, but are either ignorant of his primary interests, or powerless to further emphasize our own. It's obvious enough that Musharraf has to work in his own interests first, but it's not always known exactly what those interests comprise.
Peter Tomsen mentions elsewhere in the above interview that Pakistan's grand strategy in the region was always to destabilize Afghanistan, in order to transform it into a helpless client state. The ISI themselves installed and armed the Taliban in the first place. The idea was for Pakistan to achieve some "strategic depth" for itself, in its escalating border clashes with India. The de facto annexation of 20 million more Muslims, and some of the most impenetrable, hostile terrain on the planet was seen as a net plus by Pakistan's military planners, of whom Musharraf is the current leader, so long as he furthers their overall objectives.
Which means that they are simply biding their time, until we leave Afghanistan to continue its disintegration into medieval drug-dealing fiefdoms, and the cycle begins anew.
As an added bonus, be sure to read this interview with Pakistan's UN Ambassador Munir Akram. Amazing stuff, too much to excerpt.