dlmwrite() adds the line terminator at the end of the last line that you write. When you -append on the next call, it appends to the end -- which is to say after that line terminator.
dlmwrite() cannot be used to append columns to an existing text file. Not even if you use the range inputs: the range input creates a zero-padded matrix and writes or appends that.
You will probably need to use fopen()/fprintf()/fclose() to get the file you want.
