I've had a couple of items from my inventory seem to disappear at random, my Iron keys and another random weapon. I didn't use any of the keys on anything nor sell them or the sword.

I haven't had anything vital vanish as far as I can tell. Hopefully it doesn't happen but worse case I can use a save editor to add them back in if needed.

Is there any reason why they would just seem to disappear? Pretty sure I didn't drop them somewhere either. Haven't been able to find any info on others having this happen to them so I figured I would inquire to see if anyone has heard of this happening before?

I know that Wizardry 6 has a "swag bag" which is easy to forget. Maybe Wizardry 7 has this additional storage screen.

It does have a swag bag. The items vanished out of the swag bag actually. I checked each character and the keys and sword were gone. I suppose I could have dropped them somewhere by accident but I have no idea where or when it could have happened on my journey from New City to the Rattkin Ruins. I'll just accept that something happened to them and be happy they weren't anything important.

It just struck me as odd as I've been extremely careful about inventory management and making sure I track what I've dropped and where it was dropped in case I'd need it again.

There are enemies in Wizardry VII who can steal items from inventory (mostly Rattkins if I am not wrong). So you need to recheck inventory after fighting with those, as those could be the reason for your problem. I didn't play game much yet and I have question myself: does combat log say if enemy stole something from you or you have to check inventory manually each time?

I was not aware that they could steal items. I've never seen a combat log where it mentions something about theft, but it certainly is plausible that I missed it. Perhaps it is the ones that run away during combat that stole stuff. I guess I'll have to keep an eye on the combat log and see if I can see it happen or just check my inventory from time to time after combat to make sure nothing vital is missing.

The only thing that can actually steal your items is Blindmeis, and he doesn't do while fighting. Every time you try to pickpocket him (including the time you pickpocket the signet ring to get into Ratskell's) he'll steal some items at random. He won't steal equipped or plot-relevant items, but he can steal pretty much everything else. Once he steals them, they're functionally destroyed since there's no way to get them back.

The best way to avoid this is to drop EVERYTHING on the ground before you try to pickpocket the signet ring, and then simply never pickpocket him again. It's not possible to successfully pickpocket him anyway; it always calls the scripted event that steals your stuff and says "that tickles!" instead.

Please - anyone - how do you get something OUT of the swagbag? I accidentally put some armor in it and I need the armor but can't figure out how to get it back out of the bag. Wizardry VI.

You click the item to drag it (click, don't hold the mouse-button) and then while the item is attached to your cursor you click the swagbag icon again. This will bring back your normal inventory where you can drop the item. You can also click the left or right half of the portrait to cycle through your characters.