You can also write about your problem to the Tiled user mailing list, in which case I might have already provided an option not to include the DTD reference. For now, you're lucky that I'm reading your thread. You can probably expect such an option in the next release.
Or, since you're a Java coder too (right?), you write a patch for Tiled yourself, of course.
Thanks for next release gift
I manually edit my map file, deleting dtd reference: is not a big problem, for my little project.
I'm java coder, but i don't have so much time to spend in bugfixing other projects, sorry