After further analysis Enigma is ruled out as a cause... It's happening to other projects too. Just noticed it on Yafu.
I now think it's either BOINC (I'm running dev version 7.8.0) or Windows 10 (never seen this before upgrading to Windows 10). But then again, I've had Windows 10 for a while and it's only started happening recently as of the last few weeks, possibly a bad windows update messed things up?
Multiple file system checks give no errors, either in Windows or upon boot, and I've had no problems whatsoever with NTFS before.
Here's an example of the errors I receive
Trying to see what's wrong with that file on the slots/8 folder shows:7/31/2017 1:17:10 AM | yafu | [error] Can't copy projects/yafu.myfirewall.org_yafu/ecm63mpir230core2-64.exe to slots/8/ecm.exe: Error 5
Capture.PNG
And from there it just says I'm not the owner, it's unable to display who is the owner and trying to change any security settings doesn't work.
Make that two reboots a day...