When the Soviet Union was still in existence, the borders between the republics weren’t particularly important, although there certainly were issues over them. After the breakup of the USSR, all the individual countries agreed to accept the old Soviet borders. The problem is that quite often the borders had never been clearly delimited. Even the old international borders between the Soviet Union and other countries hadn’t been worked out; borders with China and Afghanistan in particular have been troublesome.
Another significant problem are the enclaves, little pieces of one country that are entirely surrounded by another. These aren’t unique to Central Asia, but they are more common here. Kyrgyzstan has 7 enclaves within its borders; two are Tajik and 5 are Uzbek. The larger Tajik enclave is Vorukh and the largest Uzbek enclave is Sokh. Vorukh has a river running through it that both the residents of the enclave and the residents of the surrounding area in Kyrgyzstan threaten to cut off periodically when things get rough.
The enclave that tops them all those is Sokh. It is Uzbek territory in Kyrgyzstan, but almost all the inhabitants of the enclave are Tajik. About 6 years ago the Uzbeks were concerned that the Tajik residents of the area were harboring terrorists, so they mined the enclave (Uzbekistan likes to unilaterally mine disputed borders). This obviously caused major problems because the border isn’t agreed on and innocent people were often killed by the mines. Most of the mines were removed after the IMU (Uzbek’s greatest terrorist fear) was almost completely destroyed in Afghanistan in 2002. However, there are still mines in the area and people and livestock are too often still killed there.
These enclaves create plenty of other difficulties though. Sokh in particular is troublesome because the main road through that part of Kyrgyzstan goes through it. Uzbekistan and Kyrgyzstan have tried to work out some solutions. Here is an example from a report from the International Crisis Group:
In a February 2001 meeting between Uzbek Prime Minister, Utkir Sultanov, and his Kyrgyz counterpart, Kurmanbek Bakiev, [Bakiev is now the president of Kyrgyzstan] a memorandum was signed which would have given Uzbekistan a land corridor running the 40 kilometres along the Sokh River to the enclave. This would have risked effectively making Kyrgyzstan’s Batken Province an enclave in Uzbekistan since there is almost no transport infrastructure south of Sokh. Given that Uzbekistan has instituted a visa regime with Kyrgyzstan and continues to implement tight inspections for those wishing to transit through the Sokh enclave, granting it further choke points would isolate the area and give Tashkent even more military influence.
In exchange for the corridor to Sokh, Kyrgyzstan was to receive a smaller corridor to its enclave in Uzbekistan, Barak [see here and here for articles about this enclave's troubles]. Residents there have struggled with their status, particularly after Uzbekistan instituted more stringent border controls. The 627 households of the enclave have had problems sending children out to high school since the enclave is too small to have its own, as well as problems visiting clinics and hospitals. Although the corridor would have united the enclave with Kyrgyzstan and alleviated those difficulties, after visiting the lands proposed for the swap, Kyrgyz Prime Minister Bakiev stated they were unsatisfactory compensation.
Complicating matters, the document signed by the two prime ministers was leaked to the press in April 2001 and greeted with outrage in Kyrgyzstan’s parliament and by many citizens. Bakiev defended signing the memorandum, which, he insisted, was merely a starting point for further talks. Similarly, the president’s administration maintained that the memorandum was not an agreement since it would have had to be ratified by the parliament and signed by the president before it could come into force. Publication of the memorandum, combined with the repeated incidents where Uzbekistan appeared to disregard Kyrgyzstan’s border, soured relations.
In the end, all of the enclaves are becoming more isolated, both from the country surrounding it and the country it is actually part of. Uzbekistan in particular is suspicious of any Uzbek who is not actually an Uzbek citizen.
At the time of independence, around 1.2 million ethnic Uzbeks lived in Tajikistan, mostly in the north. During the Tajik civil war many fled to Uzbekistan. They were viewed with wariness by Tashkent as having been influenced by Islamist parties in Tajikistan and were not offered any state support. As a result, as many as 70 percent reportedly made their way back to Tajikistan.