From Stargate Wiki
When the Lucian Alliance began their incursion on Destiny it dropped out of FTL in range of intense periodical radiation emitted from a binary pulsar. Every 46 minutes, 37.4 seconds a burst of radiation hit the Destiny's shields and caused a power drain as the ship routed power to bolster the shields. Due to the constant radiation and the drain on the power Destiny was unable to re-enter FTL. (SGU: "Incursion, Part 1")
It wasn't until Lt. Matthew Scott and Sgt. Ronald Greer were allowed to walk on the outside of the ship using the Ancient Inter-pressure suits were they able to reprogram Destiny's shield emitters to only protect the side of Destiny facing the pulsar and allow the ship to engage the FTL engines.
As the Lucian Alliance had gained control of the ship and forced all the surviving members of the Destiny expedition offworld, Dr. Nicholas Rush in took one last chance at taking back the ship by siphoning away power from the shields in an attempt to kill off any Lucian Alliance invaders. The leader at the time, Dannic refused to give in to Rush's demands and it wasn't until he was hot dead by Ginn were the demands met. (SGU: "Incursion, Part 1", "Intervention")