This often happens when someone is writing in Markua. The Sample.txt  instructions are for when you are writing in Leanpub-Flavored Markdown. In Markua, you need to do this differently.

At the start of a chapter you would like to include in a sample, type this:

{sample: true} 

Please note that where the sample starts, you cannot leave a blank line between the line with {sample: true} and the chapter heading on the next line that starts with #.

Here are some more in-depth instructions:

http://help.leanpub.com/author-help/how-do-i-make-a-sample-book-available-when-im-writing-in-markua