Your description indicates several possiblities. Posting some code would be useful.

You open the file read and write. You might be truncating the file before you can read from it.

You are having trouble getting past the first line, might also indicate premature end of file that can happen when reading binary files on a Windoze OS. You'll want to use binmode function to read binary files. See 'perldoc -f binmode'.

Also editing the file in place is prone to error. Some code demonstating how you are doing this would be helpful.

YuckFoo