Most fat jar approaches, e.g. Maven assembly, have problems with resources at the same location in the classpath in multiple JARs. E.g. if two JARs being bundled into a fat jar have a types.txt file, only one survives.
One option to fix this would be to change the pattern that uimaFIT uses to search for these files, e.g. from classpath*:META-INF/org.apache.uima.fit/types.txt to classpath*:META-INF/org.apache.uima.fit/**/types.txt