For the moment being, just put the idea of Barry, bcharge, btool and berry_charge out of mind; pretend they don't exist. The core problem it appears is that your device does not show up to the Linux subsystem itself; when the device is plugged in - even if nothing actually works (USB, charging, etc.) it should properly be listed as something in the output of lsusb -v. I call this the "is it plugged in?" test (regardless of what tech we're talking about).
You have a rather recent kernel, so that shouldn't be it - the core bits & pieces needed should be properly compiled. Have you tried loading the "uhci" USB subsystem for your machine instead of the "ehci" subsystem? It's very machine dependent which one you use (depends on the chips on your motherboard), this would be the first test I'd try and do. I'm not an Ubuntu guy to know how this distro allows you to "switch" the subsystems, but it's usually in /etc/modprobe.conf (if not, it's possible it's compiled into an initrd file - you'll need to Google for the specific Ubuntu way).
Google link for 'uhci ehci ubuntu" - lotsa hits:
Try also examining /var/log/messages and /var/log/dmesg when you plug in the BlackBerry - do you see any errors or messages that might help give a clue why your system isn't registering the basic connection? I think you get where I'm going - ignore all the high level tools until you can at least get some sort of lsusb -v entry showing up on your machine, somehow some way.