I am using only the repository .gitignore (repository root) and am seeing issues on Windows as well.
The problem could be related to un-ignore rules or mixed-case directory paths in the repository. I haven’t created a repro repo, but this is the general setup:
.gitignore (partial, some surrounding lines as well):
[Bb]in/
!/ext/[Bb]in/
!/ext/[Bb]in/**/*
!/somedir/[Bb]in/
!/somedir/[Bb]in/*
!/ext/src/somedir/[Bb]in/
!/ext/src/somedir/[Bb]in/*
!/somedir/[Bb]in/de/
!/somedir/[Bb]in/de/*
All files under /somedir/Bin/ show up as unstaged (even though git status doesn’t show anything and they are mostly def. not ignored and they are also part of the repo).
Another detail:
It looks like the directory paths for the files in that directory are stored with varying casing in the repo (could be an artifact of an initial svn-to-git conversion).
So there is (among the unstaged list of Sublime Merge):
/somedir/Bin/file1.dll
/somedir/bin/file2.dll
/somedir/Bin/file3.dll
… etc…
Hope this helps
Best
Tobias