Windows and Linux are eating each other

I have a dual boot. Windows is on my SSD, and ubuntu is on my HDD. The HDD is partitioned so like 90% of it is Ubuntu, and 10% is a cross system partition I call No Man's Land. I would understand if this caused issues for Ubuntu, though I have made it so windows doesn't automatically mount the ubuntu partition. Likewise, Ubuntu doesn't mount my SSD. The two OSes shouldn't be interacting directly with each other at all, only sharing files through No Man's Land. And yet, every time I switch OSes, there is some sort of issue. Windows always says it has to run a disk check, and my ubuntu desktop frequently breaks down requiring repair via the terminal. This has come to a head today when I switched to windows for some gaming and was faced with missing dlls and broken files in many games that I thought were thoroughly separated from No Man's Land and Ubuntu. Broken audio and networking drivers in Fortnite due to corrupt DLLs, Minecraft says "can't join server" when I try to launch a single player world (and can't join actual servers), and updates to steam games have thrown errors. Is this just a coincidence or is there some aspect of setting up a dual boot that I've failed at?