John Owen summarizes well my belief concerning the nature of scripture:
I affirm, That it is the work of the Holy Spirit to enable us to
believe the Scripture to be the word of God, or the supernatural,
immediate revelation of his mind unto us, and infallibly to evidence
it unto our minds, so as that we may spiritually and savingly
acquiesce therein. (Owen, J. (n.d.). The works of John Owen. (W. H.
Goold, Ed.) (Vol. 4, p. 15). Edinburgh: T&T Clark.)
First, It makes sense that the Scripture must have its authority from its own internal self and therefore be ‘self evident’ – not needing men to authorize or prove its authority. Men are useful in confirming that evidence but the original source of faith must not come from men, and therefore not from reason or logic itself, as the origin of the authority of scripture to the mind.
Second, being self evident would not imply everyone can see it – due to sin. It is collecting guilt not to believe self-evident truths from God:
18 The wrath of God is being revealed from heaven against all the
godlessness and wickedness of people, who suppress the truth by their
wickedness, 19 since what may be known about God is plain to them,
because God has made it plain to them. 20 For since the creation of
the world God’s invisible qualities—his eternal power and divine
nature—have been clearly seen, being understood from what has been
made, so that people are without excuse. (The New International
Version. (2011). (Ro 1:18–20))
Third, as the scriptures are infallible and spiritual it is the Holy Spirit alone that illuminates the mind in order for one too see the self-evincing truths within them. Those who believe remain fallible and may differ to what degree they accept the infallible truths illuminate upon their minds. Even as individuals we will always grow and learn and so may spend our lives finding more and more of those infallible truths in the scriptures as they are an endless universe of faith, hope and love.
18 And we all, who with unveiled faces contemplate a the Lord’s glory,
are being transformed into his image with ever-increasing glory, which
comes from the Lord, who is the Spirit. (NIV (2 Co 3:18).)
From this mountain peak of illuminating truth, to descend into the carnal and dirty divisions between Christian denominations who claim a different cannon of scripture: the answer is some have more genuine faith and resist the Spirits illumination less than others. And some have no faith at all.