How to vertically align my datapoints to the x-axis/prevent some from not showing up on the graph (left of the y-axis)

[#1]

(I'm using JMP Pro 16.0.0)

[#2]

I guess the time points are not the same integer value, so the curves are displaced a bit. I think if you leave the data type as numeric and the modeling type as nominal, just add the Fixed Dec format with 0 decimal places.

[#3]

You will need to change the structure of your data table.  If you split your table into separate columns for each Flour Treatment, and then drag all of those columns to the Y axis, the values will align on the X axis.  

The example below, started out with a data structure similar to your data table

Using

     Tables=>Split

the table was restructured to

When run through Graph Builder the below is the output

names default to here(1);
New Table( "Untitled 8",
	Add Rows( 24 ),
	New Script(
		"Source",
		Data Table( "semiconductor capability By (wafer, SITE)" ) <<
		Split(
			Split By( :SITE ),
			Split( :"Mean(NPN1)"n ),
			Group( :wafer ),
			Output Table( "Untitled 8.jmp" ),
			Remaining Columns( Drop All ),
			Sort by Column Property
		)
	),
	New Column(
		["en" => "wafer", "ja" => "ウエハー", "x-id" => "S_wafer_Col", "zh-CN" => "晶片"],
		Numeric( 1 ),
		"Nominal",
		Set Values(
			[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
			21, 22, 23, 24]
		),
		Lock( 1 )
	),
	New Column( "1",
		Numeric,
		"Continuous",
		Format( "Best", 12 ),
		Set Values(
			[114.178022958114, 115.41162218951, 115.974121561276, 115.183512088447,
			114.222577279334, 116.288414662737, 114.955950855513, 115.724470192397,
			114.310454140788, 114.411916363697, 115.578882257091, 115.717758425674,
			114.573856984798, 114.275626995996, 113.939489540314, 115.742033937971,
			114.309999339296, 113.67395360538, 114.956358519236, 114.236329241643,
			116.239982367895, 115.358247098562, 113.077113738801, 114.928595561162]
		),
		Lock( 1 )
	),
	New Column( "2",
		Numeric,
		"Continuous",
		Format( "Best", 12 ),
		Set Values(
			[115.146013036409, 114.882496976401, 114.851682152559, 115.131474429869,
			115.140130607274, 115.173144140875, 115.941657741059, 114.372259836792,
			114.772595594595, 114.936586576878, 114.057056049077, 115.261599036229,
			115.379516746059, 113.249023499727, 113.707629227685, 116.098584591648,
			113.8783764344, 114.507704336155, 114.919728494473, 114.18377940071,
			114.557613229875, 115.859871124488, 115.296883011271, 113.811015180155]
		),
		Lock( 1 )
	),
	New Column( "3",
		Numeric,
		"Continuous",
		Format( "Best", 12 ),
		Set Values(
			[114.301674149298, 114.413363830575, 114.397535645878, 114.167538145698,
			115.472504264664, 113.369311401258, 115.034986668101, 114.738619191954,
			114.916344256653, 115.74089466973, 115.737907348125, 114.300732573126,
			114.276625751726, 112.863280078262, 114.977428972075, 114.479998069134,
			114.515166517115, 115.494470321947, 114.797414497247, 115.548382169918,
			115.426349755613, 115.228434733636, 116.217140171491, 115.531654430536]
		),
		Lock( 1 )
	),
	New Column( "4",
		Numeric,
		"Continuous",
		Format( "Best", 12 ),
		Set Values(
			[114.469168084809, 114.695494969094, 112.906969870156, 114.887562905664,
			114.521195633807, 115.157788283074, 114.014847590677, 114.223794390975,
			114.674058445723, 114.812624602366, 115.263983985772, 115.618129210807,
			114.288160756986, 114.342808565986, 113.814302060817, 115.480129188089,
			113.073766470025, 115.121405313258, 115.046794265366, 112.975894079258,
			114.222322475451, 114.385675184537, 114.260474960707, 116.559730697831]
		),
		Lock( 1 )
	),
	New Column( "5",
		Numeric,
		"Continuous",
		Format( "Best", 12 ),
		Set Values(
			[114.750872695529, 113.161047225167, 114.816373312434, 116.622790566066,
			116.108476717208, 114.019887482548, 116.036883593208, 114.463559075643,
			116.113290433524, 114.326657976005, 112.476744530656, 116.749369748038,
			114.517767654968, 114.471621813057, 115.155567150744, 114.299322406824,
			115.174376566475, 115.207255987302, 115.898819582087, 114.870919570317,
			114.553602455502, 115.243414113583, 114.366454631986, 114.596870755494]
		),
		Lock( 1 )
	)
);
Graph Builder(
	Variables(
		X( :wafer ),
		Y( :"1"n ),
		Y( :"2"n, Position( 1 ) ),
		Y( :"3"n, Position( 1 ) ),
		Y( :"4"n, Position( 1 ) ),
		Y( :"5"n, Position( 1 ) )
	),
	Elements(
		Points( X, Y( 1 ), Y( 2 ), Y( 3 ), Y( 4 ), Y( 5 ), Legend( 3 ) ),
		Line( X, Y( 1 ), Y( 2 ), Y( 3 ), Y( 4 ), Y( 5 ), Legend( 4 ) )
	),
	SendToReport(
		Dispatch(
			{},
			"400",
			ScaleBox,
			{Legend Model(
				3,
				Base( 0, 0, 0, Item ID( "1", 1 ) ),
				Base( 1, 0, 0, Item ID( "2", 1 ) ),
				Base( 2, 0, 0, Item ID( "3", 1 ) ),
				Base( 3, 0, 0, Item ID( "4", 1 ) ),
				Base( 4, 0, 0, Item ID( "5", 1 ) )
			)}
		)
	)
);

[#4]

Update: The issue of misalignment only occurs when I add the standard error bars - is there any way to have those vertically align?

[#5]

Would it be possible for you to attach your data table?

[#6]

Here's the data - however, I think the issue lies within the addition of standard error bars for clarity so you can see all of them individually. I'm not sure now if there is a way to modify that.