What do you get when you do puts lines? That will give you a clue.
By default File.open opens the file in text mode, so your \r\n characters will be automatically converted to \n. Maybe that's the reason lines are always equal to lines2. To prevent Ruby from parsing the line ends use the rb mode:
C:\> copy con lala.txt
a
file
with
many
lines
^Z
C:\> irb
irb(main):001:0> text = File.open('lala.txt').read
=> "a\nfile\nwith\nmany\nlines\n"
irb(main):002:0> bin = File.open('lala.txt', 'rb').read
=> "a\r\nfile\r\nwith\r\nmany\r\nlines\r\n"
irb(main):003:0>
But from your question and code I see you simply need to open the file with the default modifier. You don't need any conversion and may use the shorter File.read.