This is a hard one because obviously we can't ask for logging in order to diagnose the problem, which is the normal approach for just about any other problem.
Since we can't do that, how about downloading the open-source of the product, i.e. edtFTPj/Free, and experimenting with the com.enterprisedt.util.debug.Logger class? You don't need the whole library - just the classes in the com.enterprisedt.util.debug package. In particular, search for the variable, useLog4j, to see find the places where the log4j integration is implemented. Notice that, in order to avoid an explicit dependency on log4j we've used reflection to call into it. The setupLog4j() method collects a set of references to the logging methods and stores them in the logMethods array. These are then called from the log4jLog() method when required.