if it is indeed a bug in GDB..
There are a couple of other debuggers you could try. I'm pretty sure that both of the ones I'm recommending aren't based on GDB (so if there is a bug in GDB then it isn't likely that we have that same bug).
TotalView, from my company, is available for free evaluation (or free for students) from TotalView Technologies - Evaluate Products.
Trying it out shouldn't take a lot of time, so there is little to loose.
You should be able to download it, untar it and type "install", take the license.dat you get in email, and drop it into place, then just type <install_path>/toolworks/totalview.8.6.2-2/bin/totalview <program_name>
I see that you mention using java calls, we have some experience using TotalView together with the Java interpreter to debug JNI-style programs. There is a white paper Downloading JNIDebuggingWithTotalView.pdf | TotalView Technologies on the topic on our web site that you might find useful.
For general usage I'd suggest checking out
Downloading QuickView.pdf | TotalView Technologies
Video tutorials for TotalView, MemoryScape and ReplayEngine
There is also the Sun Studio Debugger, from sun. Here is a URL Sun Studio - Program Debugging
Best of luck with your debugging.