I had the same problem and asked this question awhile ago. On my pc I have it set so other peoples debuffs don't show up when I look at the boss's health bar. When I used contagion and then smned Bahamut I noticed contagion disappeared. After awhile in raid my party told me it was still on him on their screens. I did focus target on the boss and it turned out it was still on him. I guess when garuda is sent away it is considered a 3rd party buff and not yours so it only looks like it went away.