Compiles and Runs Without New Program Behavior Exhibited

I downloaded source for the BuddySpace jabber client. I brought it
into NetBeans 5.5 with "import a Java application that was created in
a different environment." According to Keegan et al Field Guide 2 Ed.
page 71 Figure 4-1 I had obtained a CVS working directory. After
getting jars in the right place the thing actually compiled and ran
and was a working client. Then I started to make tiny changes in the
code, like adding a System.out.println in BSMainFrame.java. Long
story short, no changes I programmed resulted in any change in
program behavior, either by run in NetBeans, or run with debug in
NetBeans, or from command line. That is, what I said to print did not
print when I fully expected it to print. There are
System.out.println's in the source code that work, but mine don't
work, nor do my changes in their's work. So, I figured this must be
something I don't understand about CVS. Thus, I started all over with
a fresh copy (hundreds of source files) in a separate directory
except I systematically deleted every CVS-related subfolder, and
imported the entire modified source tree over again. Now there is no
evidence whatsoever that CVS is in the story. NEVERTHELESS, the exact
same phenomena recur. I even systematically commented out (with // )
every System.out.println in BSMainFrame.java, and yet the printouts
still appear, either inside the NetBeans output window, or in a
command line window. Be reminded, the compiled code runs perfectly
well as a jabber client. Ultimately, I intend to add very interesting
functionality to this open source code. I am completely mystified so
your advice will be most helpful, thank you.