This sounds peculiarly like the issue of "DLL Hell" on the Windows platform. Ultimately, you either hope that the shared libraries match, ship with the DLLs you need, or (as a newer option) throw your chips in with WinSxS -- where the cure might actually be worse than the disease.
Maybe the fact that Java grew out of the proprietary world is part of the reason why it doesn't play nicely with open-source/free operating systems.
It's a little different than DLL hell: most applications provide their own libraries precisely to avoid DLL hell. Rather than relying on (or trying to install) some globally-shared DLL, they include their own versions of libraries, and it doesn't matter if those versions match the versions used by other applications. (As a developer you have to worry about dependency differences between libraries, but as an application installer/user you don't have to worry about it once the developer's got everything working and bundled up). The Linux distro guys are in some ways asking Java applications to go back to a world where DLL Hell is possible, which might be good for distro packagers but would be a disaster for developers.
I think it's because Java sees itself as its own operating system, and because it started out with a pretty crummy module system that's only been incrementally improved over the years.
Maybe the fact that Java grew out of the proprietary world is part of the reason why it doesn't play nicely with open-source/free operating systems.