It's replacing file on the first pass before you print it.
file = Dir(PathToFolder)
While (Len(file) > 0)
cellOutput = PathToFolder + file
ThisWorkbook.Sheets("PDP Comparison").Cells(i, 2).Value = cellOutput
Debug.Print (file)
i = i + 1
file = Dir
Wend
Here file(file = Dir
) is just populated again at the end of the loop.