Tinderbox uses the data on the clipboard. Users are sometimes confused when pasting text from other sources to get fewer or (usually) more line ends in the resulting text than they expected.
The most common reason is that some source formats, PDF being a good example, store lines of text as just that—separate runs of text. This means that although a paragraph of text at source can be selected and copied in a tool like Preview, the data pasted is a set of lines of text not a single run of paragraph. In the same scenario a copy of multiple paragraphs will still be a set of text lines with no obvious paragraph delimiter. This is a 'fault' of the source format, not Tinderbox as some assume: there is no paragraph ending information for the application to use.
When pasting in text, it is generally a good thing to use 'Paste and Match Style' ([Cmd]+[Opt]+[Shift]+V]) instead of a normal paste. This will retain bold/italic mark-up and tabs but strip things like font typeface. It should also normalise line endings to the OS X form (more on line endings in text).