Windows Defender suddenly dishing out False positives?

[Zuperbuu]

I've been using this build of SKyrim for 2 years now, running SKSE and NMM, and moved to MO in the past 3 months. I haven't downloaded any new mods or updated mods since.

Suddenly my game scripts started to crawl, so I started a new game in belief it was savegame bloat; the script lag remained though. So I browsed the web for any help and found tweaking the Skyrim INI papyrus section helped scripts run at the expense of FPS, so I applied the tweaks someone recommended.

When I started Skyrim through MO all seemed normal, but then when I approached an NPC to start a quest Defender flagged up saying it had detected Trojan:Win32/ (I cannot remember the entire name, I deleted it ASAP).
I then played the game again and everything seemed fine until I encountered a crash that kept reappearing, so I validated Steams skyrim files and it said 6 were missing, so it reapplied them and the crashing suddenly stopped...I am thinking that Defender flagged some files from skyrim but then why was I able to run the game when usually it detects .exe's as trojans and Skyrim should only have one?

To be on the safe side I ran a scan on Defender and malwarebytes, neither detected anything. Was this a false positive? I find it odd that Defender suddenly flagged up like this when I didn't download anything...