I had the same problem (decided to use git installed under cygwin instead of the one from msysgit). Same thing: I was able to commit from the command line, and I was also able to see modification indicators and view logs in Tortoise, but I could not commit through the GUI.
What I had to do was to adjust the group settings of my project and the git executable. From one level above my project root, I ran the following command:
chgrp -R None my_project/
Then I did the following:
cd /bin
chgrp None git.exe
This changed the group of the git executable from what it was (root) to None.
Note that you may not want to use the None group. Look at /etc/passwd and look at the fourth field of the line that starts with your user name (fields are colon-delimited and the first field is your user name)--that fourth field is your primary group ID. Then look at /etc/group and find the line that has the same group ID as the third field. That's the group name you want to use (in place of None) in the commands above.
Let me know if that works for you.