Git status reports untracked on tracked files

I would be grateful for any thoughts about the follow problem.

Git status reports untracked files:

    $ git status
    # On branch master
    # Untracked files:
    #   (use "git add <file>..." to include in what will be committed)
    #
    # resource.enlighten/map/enlighten_test/.enlighten/__build_object__/geometry/land_9/processed/
    nothing added to commit but untracked files present (use "git add" to track)

But we have files at this directory at index:

    $ git ls-tree -r HEAD |grep land_9/processed/root.pim
    100644 blob 9eeca5c75dc2c945600b6e0d253a8cb8191b7e80
resource.enlighten/map/enlighten_test/.enlighten/__build_object__/geometry/land_9/processed/root.pim

I have checked this error appear after the first commit, that added this file.

I have tried:

1. Clone repo.
2. Clean/Checkout file (as described at this [1] article) - after
checkout status is untracked.
3. Copy full directory resource.enlighten/ to another repo and add
commit - no errors.
4. Run git fsck - no errors.

Git version 1.8.1.2. for Windows

Git config:

[core]
	repositoryformatversion = 0
	filemode = false
	bare = false
	logallrefupdates = true
	symlinks = false
	ignorecase = true
	hideDotFiles = dotGitOnly
	compression = 1

Thank you in advance.

[1] http://stackoverflow.com/questions/11525358/git-untracked-files-list-is-wrong