Hi all. I hope someone can help me or at least confirm I'm not crazy.

I'm playing the Gog Cut, with all the mods it comes pre-loaded with (2 of them I had to disable for stability but that's got nothing to do with this, as I noticed this on my very first run with all mods activated as well).

Everything seems great EXCEPT in every dungeon I have been in, I have come across an instance of an invisible loot pile. One place it happens for me to confirm is Privateer's Hold, when you go down the first available stairs down to a single room down (a loot pile on a pedestal on the back right wall, PLUS a spot on the floor where it says "Loot Pile" with random loot).

Sporadically I'll be in a randomized dungeon and come across this if I happen to be looking at the ground at the right time.

To be clear, this isn't "ALL LOOT PILES ARE INVISIBLE" not at all. There's just randomly occurring loot piles that happen to be so.

Sounds like a mod-related problem or a conflict between different mods.
As it happens very early in the game, I'd disable ALL mods, start a new game and check the loot pile. If it's there, you know it has to do with the mods, and you can start searching for the culprit(s) if you want to, by enabling one or several mods, trying again etc., until the loot pile has disappeared again.
If it's not there with all mods disabled, I'd un- and reinstall (or verify) the game files, or download and install DFU separately and try again.

All I can tell you that I visited this place in Privateer's Hold in probably 50 - 100 different games, in both classic DF and in DFU, and never had a problem like this. But then I don't play the DF GOG Cut at all - I prefer to have and manage my own DFU installation.