What makes the Balance of Payments (BoP) to imbalance? Theoretically the capital account balance should fully offset the current account balance and the BoP should be zero for any economy. What causes the imbalance or discrepancy in the overall BoP ? What makes countries run BoP surplus or deficits ?
This depends on the exchange rate regime. For a floating exchange rate, the balance of payments is always in equilibrium, that is, the financial account always offsets the current (and capital) account. A hypothetical deficit is avoided by a depreciating exchange rate, a hypothetical surplus is avoided by appreciation.

For a fixed exchange rate regime, the central bank will offset the exchange rate adjustments that guarantee the equilibrium under floating exchange rates. In order to offset these adjustments, the CB has to intervene in the exchange markets. To prevent a currency from depreciating, the CB has to use its foreign reserves to buy its own currency. To avoid an appreciation, the CB has to buy foreign currency and icrease its foreign reserves.

To sum up, as an answer to your question: BoP imbalances only occur in a fixed exchange rate regime and are caused by foreign exchange interventions of the CB. Therefore, the imbalance is equal to the settlements balance, or the change in the CB's reserve assets.