This post will probably get moved or removed, since unfortunately this isn't the place for that problem. Try making a new topic in our "Freelancer In General" forum. I think you might find the same trouble in the original Freelancer. It's usually all down to graphics settings in Freelancer and on your computer, try changing any of these to see if it makes a difference.
Back on topic-
marauder: Excellent research mate. I will have a quick look at the shield hit-box when I get a chance, though I very much like your idea of removing it completely. The downfalls are that you'll likely pick up a repair bill everywhere you trade due to any shots going directly to hull. The advantages however, like you've listed, are numerous and beneficial to the whole of Discovery as a roleplay mod.
People seem to forget that trading is supposed to be arduous and dangerous. If people drop their trains because of a change like this, all the better, we'll have much more diversity. Perhaps Large Trains could get a bit of a cargo hold increase to make up for the lack of shield, though only something like 6000 space (if you look at the Transport, it has 2 cargo pods and 2000 space I think, only makes sense the Large Train should have 6000 for it's 6 pods).
I hope the hitbox problem can be rectified though, as other ships also suffer similar problems with missile immunity.