OK, I think the Seizures Pending Acceptance.xlsx you've posted is what you have at the end of the macro running as you currently have it.
The formula has been inserted into E2 by the macro and the rows in the column down to row 61 appear to be empty.
If you look at this part of the macro you have
Code:
Columns("D:D").Select
Selection.Insert Shift:=xlToRight, CopyOrigin:=xlFormatFromLeftOrAbove
Columns("D:D").Select
Selection.ColumnWidth = 15
Range("D2").Select
ActiveCell.FormulaR1C1 = "=MID(RC[-3],5,4)"
Range("D2").Select
Selection.AutoFill Destination:=Range("D2:D8000")
Range("D2:D8000").Select
Columns("D:D").Select
Selection.Copy
Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
:=False, Transpose:=False
Columns("D:D").Select
Range("D2").Activate
Application.Run "enter_values"
Columns("D:D").Select
Columns("D:D").EntireColumn.AutoFit
You are inserting a new column D, making the original column D the new column E, and you never touch column E again until you insert the formula.
With the new column D, you insert a formula into D2, and autofill to D8000.
Then copy column D and paste it over itself as values.
Next you run the little "enter_values" sub which actually does the same .value=.value thing, again, on the same column.
I suspect the intention was for one of these operations to be on the old column D (the new E) and one on the new column D.
Any how, if I remove the formula from E2 and run this test macro on the sheet, things seem to be as they should be, give it a try
Code:
Sub Insert_Formula_and_Autofill()
With Columns(5)
.Value = .Value
End With
Range("E2").Select
ActiveCell.FormulaR1C1 = _
"=VLOOKUP(RC[-1],'[CBP Port and Other Agency Listing.xlsx]Combined'!C4:C5,2,FALSE)"
Range("E2").Select
Selection.AutoFill Destination:=Range("E2:E" & Cells(2, "E").End(xlDown).Row - 1)
End Sub