It happened to me once when I bought a laptop from the US. They sent me a letter telling me that it has been confiscated by the customs, and to recover it I must come to Lahore GPO. After going there, they gave me the runaround. They asked me to fill a release application which had this clause "I agree to pay all duty applicable on the item", and then get it signed by the registrar in the GPO. Afterwards, you get in the queue to customs officer. When your turn comes, the customs officer examines your item, and tries to BS you that you can't have your item. To get your item, you not only have to bribe the customs officer but also pay customs duty on top.
Rule book? This is Pakistan bro, there are no rules here. The customs officer will charge whatever he determines is right. When I got the letter from post office first I was also like you, and tried to find some source about VAT/customs duty in Pakistan. I found a page regarding duties on computers on FBR's website. The website said that imported computers are exempt from any duty, I printed the page but when I showed this page to the customs officer his tone became very stern and he said do you want to get your item or not? I had to pay the customs tax plus bribe him to get the laptop from there.
This happened in 2010.