You can run cola like this to enable debug mode:
$ GIT_COLA_TRACE=1 git cola
I don't think we have to go there, though.
It sounds like you may have stuff ignored via .gitconfig.
Compare the output of these two commands:
$ git ls-files --others
# --- vs ---
$ git ls-files --others --exclude-standard
The 1st command lists all untracked files.
The 2nd command is filtered using .gitignore, and is what cola
uses to find untracked files.
I would suggest checking your .gitignore and .git/info/exclude
files. Untracked files that match the ignored patterns will not
be displayed in the UI.
--
David