So I finished playing last night and just went to see what new quests the Companions have for me. Aelia gave me a second totem quest but I didn't do it, I replayed that save and went to her again and she gives me a kill the beast in someones house quest, why are they different every time? Will I get to do the second totem quest eventually?

"No idea."

I guess those are radiant quests, don't be lazy like me and look on the UESP..

It is called a radiant quest and this should really be in the spoilers forums not the general discussions shouldn't it?