I do not know how you manage to do this, but the line endings \r\n in your string seem to be there as 4-byte character sequences, not as 2-byte escaped CRLF. If I copy your file into a ruby string with single ticks:
unescaped='PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz48cmV2aWV3LWNhc2UgY3JlYXRl\r\nZGF0ZT0iMTMvTWFyLzIwMTQgMDk6MDQ6NTEiIHN5c3RlbT0iVHJhZmlndXJhX1RlbXBsYXRlX01h\r\nbmFnZW1lbnRfdjUuMSIgYmF0Y2hpZD0iMCIgdHJhbnNhY3Rpb25ubz0iMSIgYmF0Y2huYW1lPSJH'
Base64.decode64(unescaped)
#=> garbled text for every second line
if I do the same with double quotes (which respect the escape sequences):
escaped="PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz48cmV2aWV3LWNhc2UgY3JlYXRl\r\nZGF0ZT0iMTMvTWFyLzIwMTQgMDk6MDQ6NTEiIHN5c3RlbT0iVHJhZmlndXJhX1RlbXBsYXRlX01h\r\nbmFnZW1lbnRfdjUuMSIgYmF0Y2hpZD0iMCIgdHJhbnNhY3Rpb25ubz0iMSIgYmF0Y2huYW1lPSJH"
Base64.decode64(escaped)
#=> all is well that ends well
Therefore the problem seems to occur when you write the file. It can be amended in Ruby though:
unescaped='PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz48cmV2aWV3LWNhc2UgY3JlYXRl\r\nZGF0ZT0iMTMvTWFyLzIwMTQgMDk6MDQ6NTEiIHN5c3RlbT0iVHJhZmlndXJhX1RlbXBsYXRlX01h\r\nbmFnZW1lbnRfdjUuMSIgYmF0Y2hpZD0iMCIgdHJhbnNhY3Rpb25ubz0iMSIgYmF0Y2huYW1lPSJH'
Base64.decode64(unescaped)
escaped=unescaped.gsub('\\r', "\r").gsub('\\n', "\n")
Base64.decode64(escaped)
#=> now you should be fine again
but of course the correct solution would be to store the file correctly.
Given your current file the following should work:
require "base64"
content = File.read('Input.txt')
content.gsub!('\\r', "\r")
content.gsub!('\\n', "\n")
decode_base64_content = Base64.decode64(content)
File.open("Output.txt", "wb") do |f|
f.write(decode_base64_content)
end
Please do post some output if it does not.