Well I've decided to try out this editor and it seems like you've done some good work on it, I appreciate it.
I have some questions though. But before that, I'm using 64-bit Linux, with the openjdk-7-jre software in place of Oracle's JRE. As you can see here, I am using the version made to be compatible with stuff made for Java 7u75. More info on openjdk can be found here.
Now, first of all, I notice that the program says it is version 3.4. Is it supposed to be that way? Not that it really matters. Given the presence of the password field, it seems that I can safely say I am using version 4.1. On the other hand, I believe you said this:
"Images and database now back inside of the executable. It made much less difference to the file size than I'd expected."
And at least for the images, that does not seem to be the case for me. I had to download the images archive and extract them to an "images" folder in the same directory as the PokemonEditorGen1To3Linux64.jar file, for it to have images. That still isn't a big deal though, it just makes me curious.
Anyway, moving on. There are two significant problems that I have encountered thus far.
The first is that, while it shows the pokemon in box 1 and the items in the bag just fine, it won't show any other item category pages (such as the ball category), and it won't show any boxes other than the first one. Additionally, it won't show my party members. Now, the interesting thing about this problem is that when I used a version of the program that was probably the one just before 3.4, I am fairly sure that it didn't happen. Here are some screenshots of the problem:
Bag
Ball
Box 1
Box 2
Party
As for the second problem, the pokemon editor window is a little bunched up... I'm not too sure how to describe it very well, so here is a screenshot.
For this problem, I don't remember whether it was like this in past versions or not, unfortunately. On the other hand, if I were able to increase the height of the window more, this problem would likely go away. I would do that, but this screen is 1366x768...
Of course, these concerns are kind of pointless if you do not have any plans to support openjdk. And you obviously do not have to if you don't want; I'm not trying to force that on you. I personally value the idea of "free and open source software (FOSS)" and that's why it would be convenient for me if you did support it.