The Afghan Army is becoming another battleground in the war against the Taliban. That's because the Pushtuns, the largest minority, are not joining the army in large numbers. That's because nearly all the fighting is in the Pushtun south, and soldiers are more loyal to their tribe than to their nation. In Afghanistan, all you have is tribes, and the national government is an ongoing anarchy of deal making and attempts to keep the peace between the tribes. President Karzai is a tribal leader from one of the larger Pushtun tribes.
The Taliban are mainly from the Pushtun ethnic group (38% of the population and historically the dominant group), while many of the minorities in Afghanistan (Tajik, Uzbek, Hazara and Turkmen) have long been united in their opposition to Pushtun domination. The Tajik are 25% of the population and the Hazara (Mongols, a reminder of the medieval Mongolian invasions) 19%. The remainder are mostly various Turkic groups (Uzbeks and Turkmen). All of these groups are wary of the Pushtuns, but will work with them if they do not feel threatened.
When the Taliban took over in the 1990s, they actually controlled only southern, Pushtun, Afghanistan. The Taliban began making annual attacks into northern, non-Pushtun, areas in 1997. These attacks were repeated each year, despite a UN and American embargo to protest Taliban providing refuge for Osama bin Laden and the al Qaeda terrorist organization. The rest of the world wasn't happy with the Taliban tolerating a thriving heroin trade in Afghanistan. Most Afghans were no longer happy with the Taliban. It seems the Taliban represented religious conservatives from a few of the Pushtun tribes. The rest of the tribes didn't want to be forced to abide by the customs of those tribes. But the Taliban insisted, and used of thousands of foreigners, recruited and trained by al Qaeda, as enforcers.
When president Karzai goes on about "negotiating with the Taliban," he's talking about negotiating with the few Pushtun tribes around Kandahar, that provide most of the leadership and manpower for the Taliban. He's had a difficult job, because his government is still largely non-Pushtun at the top. When the Taliban was defeated in late 2001, it was a Northern (Tajik, Hazara, Turkic) Alliance victory. The U.S. contributed a few hundred Special Forces operatives and CIA agents, and a few thousand smart bombs.
At first, the new Afghan government tried to build its new army with troops recruited from all the major ethnic groups. But it eventually became evident that the non-Pushtuns were more enthusiastic about this. So now, the army is about 40 percent Tajik, and only 30 percent is Pushtun. Most of the senior army leadership is Tajik. Some 70 percent of the infantry battalions are commanded by Tajiks.
The basic problem is that, for centuries, the Pushtuns have dominated what is now Afghanistan (and what is now Afghanistan didn't become Afghanistan until a few centuries ago). The junior partners up north were OK as long as they knew their place (deferring to the Pushtun tribes). The Taliban upset that apple cart by making war on the northern tribes and trying to rule by force (as they believe they were ordered to do by God.). Now the northern tribes are controlling more of the central government than many Pushtuns are comfortable with. In addition, the Taliban (who represent the Islamic radicals among the Pushtuns, a group that was always there, but has grown over the last year due to radical religious missionaries, and cash, from Saudi Arabia) are still in business. The Taliban keep going because of their partnership with the drug gangs, who got started when Pakistan drove the heroin trade across the border in the 1980s.
While the Taliban are fighting with guns and terrorism, most tribal leaders are still trying to hammer our a more agreeable compromise. This has been going on since 2002, but progress is slow, as it has always been in Afghanistan. Meanwhile, the army will always be at war with itself, because of the tribal animosities.