Try this on a copy of your data, it will only copy once per area...
Option Explicit
Sub ReformatData()
'JBeaucaire 2/8/2010
'Reorganize groups of data in column A into row format
Dim i As Long, RNG As Range
Application.ScreenUpdating = False
Set RNG = Columns("A:A").SpecialCells(xlCellTypeConstants)
For i = 1 To RNG.Areas.Count
RNG.Areas(i).Copy
Range("B" & i).PasteSpecial xlPasteAll, Transpose:=True
Next i
Columns(1).Delete xlShiftToLeft
Application.ScreenUpdating = True
End Sub
It blew through 5500 rows of data, 650 "groups" in about 3 seconds.
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