Before you start throwing files at the folder, are you
sure you're recycling the tube? After the shot, try clicking on the muzzle door "box" on the status panel to shut it. The tube should automatically drain and de-pressurize and you should be able to reload.
If that doesn't work there's one more thing I can think of. Go to the game's main screen and enter a new player name. Try running a Seawolf mission again and see what happens. Your old name will still be there but you'll be playing as a new character. I'm wondering if your old "name" (actually the save files) may have been corrupted at some point?
Otherwise, you may need to do a fresh install of DW then run the RA mod installer again. What you're describing sounds like something fundamental ain't right. If you have to re-install, try the Seawolf prior to updating to RA and make sure it works. Then, run the RA install and make sure everything installs correctly. There should be an installer "DOS box" that will scroll through a bunch of text as the installer does its thing. When it finishes, you may get a message saying "type Y to quit" or the installer should shut itself down automatically. BTW, the installer should take a while (something like 4 or 5 minutes) to run.