Your manifest looks good as you're using Import-Package to pull in commons logging.
How are you driving the code that contains to logging calls? dm Server is aware of a number of entry points into the server, and at these entry points it sets up some thread-based context that's used by the per-application trace routing. The entry points of which dm Server is aware include requests received by Tomcat, and during application deployment.
One entry point that is not covered is any logging that triggered as a result of using the telnet console. E.g. if you stop or start a bundle using the console and it performs some logging in its activator, this logging will not be routed to the per-application trace file as dm Server doesn't have an opportunity to set up the appropriate context.