When you open JSGME, in the center of the panel, below the arrow keys, there is a link titled "Tasks"; click on that and select "Generate snapshot of game files".
Also, if you are using a "super-mod" such as GWX or NYGM or w/e, remember that those mods alter LOTS of the games original files. So if you add mods after one of the super-mods, it is very likely some files will be altered again. So, don't be surprised. Many mods here in the download section will specifically say if they are compatible with the popular super-mods, and often will give advice regarding what order to enable them in.
And, always remember, if you are adding mods and intend to continue a career you have already started, ONLY add the mods when your captain is in port, between patrols; otherwise you will have issues with your saved games-the file configuration will have changed, and the save will no longer be compatible with your new mod list.
Good luck!
