If you do a 'savesas' and choose the first 'text type' it will create a tab delimited file. This means that at the boundary of each cell it will insert a tab character. When you look at the resulting file using a text viewer (like notepad) these tab characters will make it look like the columns don't line up.
Have you tried to 'saveas' a 'formatted text' file (aka space delimited)? This will give you an output file that makes all the cells in the same column equal in size. It will fill in with extra spaces to make everything line up.
Keep in mind though that if you use a program like notepad to look at your text file you may still see jagged columns. If this is the case then try setting the viewing font in notepad to a fixed width font like Lucida Console.