I assume you are currently writing your data in a numeric matrix? If you require your data to be separated by a column, you could prepare all of your data into a cell array and write that to file, giving you much more control of the format I believe.
Write Microsoft Excel spreadsheet file - MATLAB
I haven't tried it, but give the cell array method a shot and see how you get on. Worst case scenario is you can format the data in excel with a few lines of VBA.