The LHC is filled through two 3 km long transfer lines from the last pre-injector, the SPS. During the LHC proton run 2011 large drifts, shot-by-shot and even bunch-bybunch trajectory variations were observed with the consequence of high losses at injection and frequent lengthy trajectory correction campaigns. The causes of these instabilities have been studied and will be presented in this paper. Based on the studies solutions have been proposed. The effect of the solutions will be shown and the remaining issues will be summarized