I assume you already checked carefully? There are a couple items which are either small or coloured similar to the background of the inventory window, which can make them hard to spot.
Try moving your mouse down the right edge of the inventory, to see if you can catch the end of something. I ran into this problem once as well, though in an unpatched game, after really loading a barrel with loot. I thought this was subsequently fixed, but obviously not completely. Did you install the patch before starting the game, or after you ran into this problem? By moving the mouse cursor slowly along the right edge of the inventory I was able to catch the edge of a spear when the description popped up (though the spear itself was not visible), but lost a couple other items. Fortunately I was only dumping miscellaneous stuff in there to sell later.
After that I was careful about piling too much stuff in one spot, since the problem only appeared when something was dropped in a very crowded inventory, so it could not fit where dropped or close by.
With the 1.47 patch the weight penalty was changed, so that you can carry more than your capacity, but can not move when so encumbered. This means you can dump most of your loot into a summoning doll's inventory (though not quest or unique items), and have much less stuff to store in barrels for later use (equipment you don't meet the requirement for yet, spare potions or arrows, etc).
If you are missing any quest items, you can get a replacement (
Inventory files), though that doesn't sound like a problem.
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