It'd probably be easier to answer your question if you included the coding. It looks like the amount of spaces/enters used for the last column to align it properly isn't correct, though that'd be weird as I'm guessing you use the same amount as for the first column.
Code:
[center][size=7][color=#EFF093]- - -[/color] [color=#4D7841]︻デ┳═ー[/color] [color=#EFF093]- - -[/color][/size][/center]
[center][columns][size=5][color=#EFF093]Introduction[/color]
[nextcol][color=transparent]|||[/color][nextcol][size=5][color=#EFF093]Runes[/color]
[color=#4D7841]|[/color] [color=#EFF093]Masteries[/color] [color=#4D7841]|[/color]
[color=#EFF093]Summoners[/color]
[nextcol][color=transparent]|||[/color][nextcol][size=5][color=#EFF093]Abilities[/color]
[color=#4D7841]|[/color] [color=#EFF093]Items[/color] [color=#4D7841]|[/color]
[color=#EFF093]Supports[/color]
[nextcol][color=transparent]|||[/color][nextcol][size=5][color=#EFF093]Early Game[/color]
[color=#4D7841]|[/color] [color=#EFF093]Mid Game[/color] [color=#4D7841]|[/color]
[color=#EFF093]Late Game[/color]
[nextcol][color=transparent]|||[/color][nextcol][size=5][color=#EFF093]Conclusion[nextcol][/columns][/center][/color]
[center][size=7][color=#EFF093]- - -[/color] [color=#4D7841]︻デ┳═ー[/color] [color=#EFF093]- - -[/color][/size][/center]
As I thought, the issue is the amount of enters you use. You have an enter between your chapter titles and the next [nextcol] tag everywhere except for near the end (after 'Conclusion'). Add one there, too:
Edit: You could also add an extra enter to the beginning of every column, which imo looks even better if you 'highlight' it with your mouse (not sure what the proper word is to describe what I mean, so I'll just show it in the form of an image):
example
Code:
[center][size=7][color=#EFF093]- - -[/color] [color=#4D7841]︻デ┳═ー[/color] [color=#EFF093]- - -[/color][/size][/center]
[center][columns][size=5][color=#EFF093]Introduction[/color]
[nextcol][color=transparent]|||[/color][nextcol][size=5][color=#EFF093]Runes[/color]
[color=#4D7841]|[/color] [color=#EFF093]Masteries[/color] [color=#4D7841]|[/color]
[color=#EFF093]Summoners[/color]
[nextcol][color=transparent]|||[/color][nextcol][size=5][color=#EFF093]Abilities[/color]
[color=#4D7841]|[/color] [color=#EFF093]Items[/color] [color=#4D7841]|[/color]
[color=#EFF093]Supports[/color]
[nextcol][color=transparent]|||[/color][nextcol][size=5][color=#EFF093]Early Game[/color]
[color=#4D7841]|[/color] [color=#EFF093]Mid Game[/color] [color=#4D7841]|[/color]
[color=#EFF093]Late Game[/color]
[nextcol][color=transparent]|||[/color][nextcol][size=5][color=#EFF093]Conclusion
[nextcol][/columns][/center][/color]
[center][size=7][color=#EFF093]- - -[/color] [color=#4D7841]︻デ┳═ー[/color] [color=#EFF093]- - -[/color][/size][/center]
- - - ︻デ┳═ー - - -
Introduction |
||| |
Runes | Masteries | Summoners |
||| |
Abilities | Items | Supports |
||| |
Early Game | Mid Game | Late Game |
||| |
Conclusion |
- - - ︻デ┳═ー - - -
Edit: You could also add an extra enter to the beginning of every column, which imo looks even better if you 'highlight' it with your mouse (not sure what the proper word is to describe what I mean, so I'll just show it in the form of an image):

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Whyyyyyyyyyyyyyy? conclusions column is uneven