I found VS was holding an .opendb file open, causing a permissions clash when searching for changes. It reported the precise file that was causing the trouble in the Output window, under “Source Control – Git”. Adding this to my .gitignore fixed the issue. If a VS restart or a reboot fixes the issue then you’re probably closing the offending file handle — in my case VS opened the problem file every time.
See also Visual Studio TFS Git not seeing any changes for more potential causes.