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 thinks like font typeface.
If the pasted text has unwanted line ends, you can use the Remove Line Breaks ([Cmd]+[Opt]+[Return]) on the Edit menu. Before doing so, if the test includes multiple paragraphs, add an extra Return at the end of each paragraph break. Thus, when Remove Line Breaks runs, double line ends revert to a single line end, retaining the paragraph structure. If the existing pasted text includes spaces at the end of lines (sometimes the case) you may notice double-spacing between words that are at the previous line breaks as Tinderbox replaces the line end character with a space.
More on line endings in text.