繰り返し処理の途中で飛ばされてしまいます。

最後が３つの組にならない場合の範囲を変化させるため。Dim w以下で数式を上書きされているようですが、ここの部分にバグがあり、特定の場合に想定しない式または数字が上書きされています。

Average関数は空白セルを無視するので、最後が３つの組にならない場合であっても、数式をあえて変化させる必要はありません。

（赤色に塗られている行は削除）

Sub 表作成()

Dim i
For i = 1 To 3
Sheets(i).Select

    Range("T1").Value = "西進(6H)"
    Range("U1").Value = "経度平均(12H)"
    Range("V1").Value = "西進(12H)"
    Range("W1").Value = "経度平均(24H)"
    Range("X1").Value = "西進(24H)"

    Columns("U").ColumnWidth = 12
    Columns("V").ColumnWidth = 8.5
    Columns("W").ColumnWidth = 12
    Columns("X").ColumnWidth = 8.5

    Dim t
    For t = 3 To 100
            If Cells(t, 8) = "" Then
               Exit For
            End If

    Cells(t, 20).Value = "=IF(H" & CStr(t) & "-H" & CStr(t - 1) & "<0,""0"",""1"")"

    Next t

    Dim u
    For u = 2 To 100
            If Cells(3 * u - 4, 8) = "" Then
               Exit For

-            ElseIf Cells(3 * u - 3, 8) = "" Then
-               Cells(u, 21) = Cells(3 * u - 4, 8)
-               Exit For

-            ElseIf Cells(3 * u - 2, 8) = "" Then
-               Cells(u, 21).Value = "=AVERAGE(H" & CStr(3 * u - 4) & ":H" & CStr(3 * u - 3) & ")"
-               Exit For
            End If

    Cells(u, 21).Value = "=AVERAGE(H" & CStr(3 * u - 4) & ":H" & CStr(3 * u - 2) & ")"

    Next u

    Dim v
    For v = 3 To 100
            If Cells(v, 21) = "" Then
               Exit For
            End If

    Cells(v, 22).Value = "=IF(U" & CStr(v) & "-U" & CStr(v - 1) & "<0,""0"",""1"")"

    Next

-    Dim w
-    For w = 2 To 100
-            If Cells(5 * w - 8, 8) = "" Then
-               Exit For

-            ElseIf Cells(5 * w - 7, 8) = "" Then
-               Cells(w, 21) = Cells(5 * w - 8, 8)
-               Exit For

-            ElseIf Cells(5 * w - 6, 8) = "" Then
-               Cells(w, 21).Value = "=AVERAGE(H" & CStr(5 * w - 8) & ":H" & CStr(5 * w - 7) & ")"
-               Exit For

-            ElseIf Cells(5 * w - 5, 8) = "" Then
-               Cells(w, 21).Value = "=AVERAGE(H" & CStr(5 * w - 8) & ":H" & CStr(5 * w - 6) & ")"
-               Exit For

-            ElseIf Cells(5 * w - 4, 8) = "" Then
-               Cells(w, 21).Value = "=AVERAGE(H" & CStr(5 * w - 8) & ":H" & CStr(5 * w - 5) & ")"
-               Exit For
-            End If

-    Cells(w, 23).Value = "=AVERAGE(H" & CStr(5 * w - 8) & ":H" & CStr(5 * w - 4) & ")"

-    Next w

    Dim x
    For x = 3 To 100
            If Cells(x, 23) = "" Then
               Exit For
            End If

    Cells(x, 23).Value = "=IF(W" & CStr(x) & "-W" & CStr(x - 1) & "<0,""0"",""1"")"

    Next x


Next i

End Sub

あえて、最後の数字の組数に応じてAverage関数の範囲を変化させたいならば、Dim u以下は下記のようにすればよいと思います。
（Dim wの段は削除）

    Dim u
    For u = 2 To 100
            a = Cells(3 * u - 4, 8)
            b = Cells(3 * u - 3, 8)
            c = Cells(3 * u - 2, 8)

            If a = "" Then
                Exit For
            ElseIf b = "" Then
                k = CStr(3 * u - 4)
            ElseIf c = "" Then
                k = CStr(3 * u - 3)
            Else
                k = CStr(3 * u - 2)
            End If

    Cells(u, 21).Value = "=AVERAGE(H" & CStr(3 * u - 4) & ":H" & k & ")"
    Next u