Hey actually something like that happened to me once with the Github for Windows. Well at least for what I understand is that the file doesn't get added to the remote git repo.
I would start the git shell:
Open the repo you're working on >> Tools and Options (Button) >> Open a shell here
There try this to see if file is added to the repo:
git ls-files yourService.exe --error-unmatch
if not try figuring out if it's ignored some how:
git check-ignore -v -- yourService.exe
if you get nothing, it's not ignored. If you do get output it is ignored somehow.
So first if it's ignored force add it manually:
git add -f yourService.exe
Now commit and push it to the server. In case you've never done this manually use:
git commit yourService.exe "This is a commit message for one file only..."
(For commiting on a specific file)
or if you want to commit on all changes and added files use:
git commit -a yourService.exe "This is a commit message for all changes and added files..."
In the case it's not even ignored you may have merge problems with the server, in that case you have to to force push to server by using: git push -f <remote> <branch>
(e.g. git push -f origin master
) which is very well explained by Trev Norris here: Force "git push" to overwrite remote files.
After that it should be solved, I kinda stopped using Github for Windows because of these ignore issues (which might be purposely developed but I do it manually and use www.github.com for visuals).
Hope this helps you.