The original post has been updated with some code but not enough of the input file was provided and kennethk's other questions weren't answered.

The description is confusing because you don't tell us things like what defines a header, what kind of data comes after the header, etc. Are the headers always all text? Or are there numbers or punctuation? Is the data always just numbers? If you can explain the problem in English then you are halfway there for writing the code.

My guess as to why it won't output the last section is because your existing code only writes to output when it sees a blank line. If the input file ends without a blank line then no output.