SSIS parses column by column, not rows then columns. There are a fair number of posts on this. Basically the work around today is to bring in each row as a single string column, then parse it into indiviudal columns in the package.
Example here: http://agilebi.com/cs/blogs/jwelch/archive/2007/05/08/handling-flat-files-with-varying-numbers-of-columns.aspx
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