There are some basic rules you need to follow for any mod. Assuming you have basic knowledge of running your computer, making folders, copying files and using windows to look around.. you should:
0. (all programmers know to start counting at zero) Have a clean working installation of the game, patched to the latest version you can afford.
1. Read instructions for both the JSGME and the mod. Read any and all instructions before beginning any actions anywhere in the entire instruction sequence so you know whats coming before you screw it up.
2. Analyse your collection of mods descriptions and know if you are using two sound or two graphic mods together, which will cause your first set of troubles and conflicts. One mod might be erased by the next mod being installed if they reference the same sound or graphic file - and JSGME will alert you to this mistake, and will also give you an "undo" feature which is nice. Best testing procedure is to unload all mods and test only the new mod by itself. Adding a few mods at a time afterwards as long as you can take notes on the conflict alerts JSGME is giving you.
3. Proceed to the forums to ask any and all questions before taking any actions anywhere in the sequence of instructions so you dont screw it up without reading all the previous support suggestions of others who can help you screw it up faster. Then send messages to the original modder and get it straight from the old salt himself. Try not to clog up the thread with needless "I need help!" messages, because a private message keeps your specific needs sorted in the PM message box without everyone else laughing at your mistakes knowingly.
If the modder is unwilling or unable to help, return to whining publicly in the event some other kind soul will step in and help stop the thread from clogging further.
4. Make backups while game is shut down. (the wisest thing I've seen written in these forums is to copy your entire stock "data" folder to a safe place, once you install gold or uboat missions, which means you are at a perfect 1.5 version starting point for mods. The reason to copy it entirely, is, so you can revert back just as if you did a clean reinstall of the game, but it is much faster than a full install in the event your hard drive starts listing, or worse, sinks beneath the waves.
5. Install the files with JGSME. Wait. Dont. First, get the latest version of JSGME and then recursively start again at the beginning of this instruction. If you already have the latest version, jump to next line.
6. Start the game and load your previous position/save game which places you in the naval office, not out to sea on patrol.
7. Then click mission map on the wall, to start mission and go to the sub on the water (which loads additional files unkown to some people). If this doesnt work, you can shut down the game completely, undo with JSGME, then redo with JSGME, and restart game.
8. For a sound mod, carefully check all your volumn controls on your headset, wires, speakers, windows control panel, etc.. this is important. Set volumn to mid-low and increase slowly to save your ears if the modder made a volumn mistake
Especially when firing gun sound mods. The dried blood coming out of my ears speaks to experience on this. I know what Im talking about, but I cant hear what youre saying right now.
9. Did you read the part about reading all instructions before taking any action? Did you take note of the part where I said take notes? If JSGME gives you any clues or error messages, tell the modder (take a screenshot, or cut 'n paste the notes) before taking any further action. These will greatly speed up the process of getting you back into "the action" you really are interested in.
PM me if you have done your homework, read every similar problem and solution you could find, and you know for a fact your virus definitions are up to date. You never know.. a gremlin might be causing your trouble.