Software testing is sometimes plagued with intermittently failing tests and finding the root causes of such failing tests is often not trivial. This problem has been widely studied at the unit testing level for open source software in the literature, but there has been far less investigation of system level testing of industrial embedded systems. This study aims at understanding, explaining and categorizing the root causes of intermittently failing tests in the embedded systems domain. We investigated a currently-running industrial embedded system, and studied system level testing in that domain. We devised and used a novel metric for classifying test cases as intermittent. From more than a half million test verdicts, we identified intermittently and consistently failing tests, and identified their root causes using multiple sources. We found that about 1-3% of all test cases were intermittently failing. From analysis of the case study results and related work, we identified nine factors associated with test case intermittence. In general, a fix for a consistently failing test removed a larger number of failures detected by other tests than a fix for an intermittent test. More effort was needed to identify fixes for intermittent tests than for consistent tests. An overlap between root causes leading to intermittent and consistent tests was identified. Many root causes of intermittence are the same in embedded systems and open source software. However, when comparing unit testing to system level testing, especially for embedded systems, the test environment itself is often the cause of intermittence.