It appears that my Java port of the Krokodile Commander software generated almost no interest at all I guess all the people who were previously asking for a Java version on the forums were actually just wanting a Mac OS X version. Nonetheless, I have done some more work on the Java version to add multicart support, and increase the transfer speed. The new version is attached to this entry, and the documentation is contained in a README file inside the zip. It is still a command-line application, but it now has essentially the same feature set as the OS X version, except for the cart database. This is probably as far as I will go with this as it now does everything that I want with the software. However, if anyone else would like to improve it, e.g. add a GUI, then they are more than welcome to modify the source code.
EDIT: I have attached a precompiled version of the jkrok software for Linux x86 below. Instructions are in the README inside the zip. Let me know if there are any problems, as this was done in a hurry!