Fixing issue with prepare method. The issue was that [stripped_contents.length..-1] was not capturing the trailing contents as expected. Instead it was grabbing the last 2 characters of my identifier block and then tacking those 2 characters back on to the end. In short, .length and the range operator are not behaving consistently on the input.

lib/whenever/command_line.rb

@@ -108,11 +108,15 @@ module Whenever
     end
     
     def prepare(contents)
-      # Some cron implementations require all non-comment lines to be newline-terminated.
-      # Preserve any whitespace at the end of contents. (issue #95)
-      stripped_contents = contents.strip
-      tail = contents[stripped_contents.length..-1]
-      stripped_contents.split("\n")[@options[:cut]..-1].join("\n") + tail
+      # Strip n lines from the top of the file as specified by the :cut option.
+      # Use split with a -1 limit option to ensure the join is able to rebuild
+      # the file with all of the original seperators in-tact.
+      stripped_contents = contents.split($/,-1)[@options[:cut]..-1].join($/)
+
+      # Some cron implementations require all non-comment lines to be newline-
+      # terminated. (issue #95) Strip all newlines and replace with the default 
+      # platform record seperator ($/)
+      stripped_contents.gsub!(/\s+$/, $/)
     end
     
     def comment_base