Paragraph Style Causing Uneven Line Lengths

Looks to me like Balance Ragged Lines might be turned on? That setting tries to make all lines the same length, which doesn't sound like what you are looking for. It's in the "Indents and Spacing"section of your paragraph style. 

Actual runt prevention techniques might include using the GREP tab of the Find/Change dialog to find the last two words of any paragraph and insert a non-breaking space between them, or to use a GREP Style to apply a Character Style with No Break to the last words of any paragraph.