git repository ignoring all .dlls

Do you have either ~/.gitignore_global or ~/.gitignore in your home directory which could also be listing these file patterns?

See https://help.github.com/articles/ignoring-files

If you use SourceTree and the default setting it will ignore all DLLs by default... Tools=>Options=>Git then "Edit File"... add a "#" before .dll => "#.dll" ... save and close.

Then for Windows Explorer in your packages folder in open a GitBash terminal and type "git add ." and let it work, back into SourceTree wait a second and all those missing package DLLs will show up for you to commit and push.

I could add the .dll files manually, but they should be tracked. Why are they not being tracked?

No, they shouldn't be tracked, unless you've added them. Only files which are already added and committed are tracked; that's what "tracked" means.

Try manually adding one of them via git add and it will tell you why it's ignoring them, and prompt you to use git add -f to add the file anyways.