Software process improvement (SPI) is an instrument to increase the productivity of, and the quality of work, in software organizations. However, a majority of SPI frameworks are too extensive or provide guidance and potential improvement areas at a high level, indicating only the symptoms, not the causes. Motivated by the industrial need of two Swedish automotive companies to systematically uncover the underlying root causes of high-level improvement issues identified in an SPI project-assessing inter-departmental interactions in large-scale software systems development-this paper advances a root cause analysis (RCA) method building on Lean Six Sigma, called Flex-RCA. Flex-RCA is used to delve deeper into challenges identified to find root causes as a part of the evaluation and subsequent improvement activities. We also demonstrate and evaluate Flex-RCA's industrial applicability in a case study. An overall conclusion is that the use of Flex-RCA was successful, showing that it had the desired effect of both producing a broad base of causes on a high level and, more importantly, enabling an exploration of the underlying root causes.