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In Timeline 5, Madoka continually goes out of her way to seek Homura out for guidance and help.
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I'm not sure about "continually", since their conversation in episode 5 looks like the only time Madoka initiated the meeting (or at least seemed to be the one initiating it). Otherwise, she interacted with Homura just because Homura was around (and she was around a lot). Of course, I also recall their conversation in episode 7... but if Madokas also initiated that one, that is because of Homura clearly proving to know what most Puellae Magi have not the slightest idea about, rather than because of vague subconscious memory.
Madoka doesn't really need to seek Homura's guidance, it's Homura's best interest to provide that guidance whenever possible. She could not bother about it until Madoka met Kyuubey, but afterwards she has to balance between trying to open her friend's eyes and spiraling down the Cassandra path again (something she clearly doesn't want).
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In fact, Homura's memory across the timelines is itself a kind of delusion, since there can be no relation between the timelines: each one substitutes and annihilates its predecessor.
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Urobuchi himself suggested/hinted that Homura's wish might be creating alternate dimensions one by one. Heh, that would make Homura a slider rather than a time traveller...
But it justifies her memories quite well. And it even provides a slightly more solid ground for Madoka's flashbacks and dreams (huh, Asura Cryin', anyone?
).