it sounds like your clojure.tools.logging is using a different underlying logging implementation than the rest of your application?
for example if your application is using java.util.logging, but you have a stray log4j library in your classpath, then clojure.tools.logging would detect log4j and would therefore not react to the logging config changes you were making.
the logic for detecting the underlying logging implementation is here:
(defn find-factory "returns the first non-nil value from slf4j-factory, cl-factory, log4j-factory, and jul-factory."  (or (slf4j-factory) (cl-factory) (log4j-factory) (jul-factory) (throw ; this should never happen in 1.5+ (runtimeexception. "valid logging implementation could not be found."))))
it would be helpful to run
mvn dependency:tree or
lein deps :tree to see what logging dependencies are on your classpath.
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