Theory

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Eric = Bill, Rachel = Charlotte Theory
A common theory that has been floating around which suggests that each of the five main characters: X, Bill, Charlotte, Rachel and Eric, talk in their own Vigenère cipher. However, due to inconsistencies, we were unable to piece together who was using which of the 5 more common keys.

Keys

 * 1) "argentina"
 * 2) "pangent"
 * 3) "conscioushumansouls"
 * 4) "signalandnoise"
 * 5) "iloveyoulottie"

Misconception
Due to "Eric" talking about his code as "conscioushumansouls", and saying that "Rachel's" code was "argentina", we assumed that the following was the correct sequence. The problem here was that "Rachel" claims her husband was Bill, but Bill's code suggests that he is unfaithful, which we have no proof of.
 * 1) Eric "conscioushumansouls"
 * 2) Rachel "argentina"
 * 3) Charlotte "signalandnoise"
 * 4) Bill "iloveyoulottie"
 * 5) X "pangent"

New Information Surfaces
Charlotte indirectly revealed that her code is "argentina" when she starts running the Twitter scripts but continuously fails. Paired with the knowledge that when being uploaded to the cube, you lose some memories, it is entirely possible that "Eric" was not actually Eric, and that "Rachel" was also not Rachel.

As of 19 February 2016, we know that the woman running the Tumblr account is Charlotte. She says that the "messages she couldn't see" with key “argentina” is hers, so Charlotte’s ciphers are “argentina”.

Eric is in love with Charlotte, evidenced by asking Charlotte out on a Christmas date, spending time with her when she was working overtime, therefore Eric's key is “iloveyoulottie”.

The only other male we know who is missing is Bill. Bill died long ago, was uploaded by Charlotte but thinks that he’s Eric. "Eric"/Bill says that his password is “conscioushumansouls”.

Between Rachel and X, there’s only left 2 codes; “signalandnoise” and “pangent”

Since X seems to be more work related, his key is more likely to be “pangent” than “signalandnoise”

Also, the twitter was run by X, which has a photo of a “pangent”.

Therefore, my solution to this is as follows:
 * 1) Charlotte “argentina”
 * 2) Eric “iloveyoulottie”
 * 3) Bill “conscioushumansouls”
 * 4) Rachel “signalandnoise”
 * 5) X “pangent”

Additional explanation: (added by kuurbis)
The original theory of Eric being plugged into the cube at some point in the past does not add up with the following evidence: These facts suggest that the timeline is instead as follows: This is countered by the fact that "Rachel" or Charlotte, while in the Cube, seems to recall Bill being her husband but not Eric. Perhaps they were married until Bill died in the accident, but we currently have no evidence that Charlotte was ever married to anyone.
 * 1) Charlotte is running the tumblr.
 * 2) Charlotte is only currently being involved with someone named "E"
 * 3) Charlotte posts "I miss Bill"
 * 4) Charlotte posts that she remembers the accident and has a scar from it.
 * 1) Bill has been dead for some time, involved in a car accident that severed his neck.
 * 2) Charlotte plugged him into the Cube (see video of her describing this act) but does not know if it worked.
 * 3) Eric begins pursuing a romantic relationship with Charlotte.
 * 4) Charlotte gets fired, has meltdown (see video).
 * 5) Something happens to Charlotte where she is uploaded to the Cube.
 * 6) Bill, in his loneliness, takes some of her memories to trick her into falling for him. He takes "too many and too many of the wrong ones" and loses his sense of identity.
 * 7) Charlotte no longer remembers who she is or who Eric is.