As of Version 1.3, the documentation has been ported to HTML. It is available in the docs directory of your download. It has also been provided online.
If you have Java installed, but the jFlagCap file isn't working for you, you should visit the Sun Microsystems homepage and download the latest version of the Java Runtime Environment (J2SE JRE) for your machine. Your problem most likely stems from not having the latest version of Java.
There are a few known quirks in the game, none to be enough to hinder gameplay. The Help tab should provide enough information for general game-play, making themes and maps and doing other related things. Feel free to contact the author (see below) for additional help.
There are many new features in Version 1.3. Problems are to be expected. However, there are many bugfixes that Version 1.3 fixed.
The game and this website are both made by Mark Burger (currently seeking employment.) Feel free to contact either me or the jFlagCap forum if you have any questions or comments. If you prefer chat, I am on ICQ at 119420913.