At the moment, as raised here https://groups.google.com/d/msg/checker-framework-discuss/uCBCRVcpM_w/VuNEI-XwBQAJ, one currently has to sometimes include both checker-qual.jar and checker-compat-qual.jar.
Some classes are contained in both .jar files, causing issues.

Each -qual.jar file should be self-contained and contain all necessary classes.