Nevermind all! I found the problem! And blimey, it's a weird one
Maybe this post'll help others if this happens to them. Regardless, thanks Martinuzz & Novaris for helping put ideas forward though, much appreciated!
Essentially, I had noticed for a long time now that in my creatures screen, I had 3 tamed vermin that I most certainly did not buy or catch. I couldn't even locate them at the time (forgot how to until just now), which was the stem of my epiphany.
I started to go through my Enhanced Stock of barrels, and found at bottom, there was a collection of barrels marked in red, similar to the following image for anvils:
However, when I zoomed to the location, it just pulled me to a unique random edge of the map each time I tried. Clearly, it was not on the map, but still registered as part of my colony. As a result, when it came to the barrels, I assumed that my dwarrows were all path-finding to barrels that were well & truly unobtainable. So, I marked the red barrels for dumping, DFHack autodumped them as there was obviously no direct path, and then checked the stocks screen. They were all still red, & glitchy. Consequently, I atom smashed them, and the problem was fixed.
Now I'm going to have through every single stock item (as these red objects are littered across them) and autodump everything this random caravan (years & years ago, denoted by the pet vermin's age in my stock) glitched out of my game.
Edit: From the wiki, Red means: "Not owned by fort (uncollected webs, and trade goods and equipment currently owned by traders or invaders)". 2.5k cave spider silk was red (caverns...) but I still atom smashed them.. let that be a lesson to red stocks!