To debug lock timeout errors, set derby.locks.monitor=true and derby.locks.deadlockTrace=true in derby.properties. This will print the lock table information to the derby.log when the timeout happens. If you also set derby.language.logStatementText=true, then all the statements executed on the system will be written out to the derby.log
The log file containing the information referenced will usually be the one named with the hostname on which Tomcat is running. On a simple server (e.g. development environment) this is localhost.<datestamp>.log