I've reproduced this by setting up a fresh Jenkins install.

Here are my notes from that install:

On Ubuntu 12.04.4 LTS

sudo sh -c 'echo deb http://pkg.jenkins-ci.org/debian binary/ > /etc/apt/sources.list.d/jenkins.list'
wget -q -O - http://pkg.jenkins-ci.org/debian/jenkins-ci.org.key | sudo apt-key add -
sudo apt-get update
sudo apt-get install jenkins

Visit http://host:8080/configureSecurity/
Check "Enable security"
Under the "Access Control" section choose the option "Jenkins’ own user database" under the "Security Realm" header.
Choose "Save" at the bottom of the page.

Visit http://host:8080/signup
Fill out form matching the username to your github username.

Return to Visit http://host:8080/configureSecurity/
Under the "Access Control" section unselect "Allow users to sign up" under "Jenkins’ own user database" which is under the "Security Realm" header.
Under the "Authorization" heading select the option "Logged-in users can do anything".
Choose "Save" at the bottom of the page.

Visit http://host:8080/pluginManager/
Select all plugins with available updates using the link at the bottom of the page and then "install without restart".
On the subsequent screen choose "Restart Jenkins when installation is complete and no jobs are running."

At this point running the following produces no error:

curl --url http://host:8080/user/mr-c --user mr-c:${api_token}

Install the Github OAuth Plugin (grabs the GitHub API Plugin)
Return to Visit http://host:8080/configureSecurity/
Under the "Access Control" section choose the option "Github Authentication Plugin" under the "Security Realm" header.
GitHub Web URI: https://github.com
GitHub API URI: https://api.github.com
Client ID: <masked for security>
Client Secret: <masked for security>
Under the "Authorization" heading select the option "Github Commiter Authorization Strategy".
Admin User Names: mr-c
Participant in Organization: ged-lab
Grant READ permissions to all Authenticated Users: yes
Grant READ permissions for /github-webhook: yes
Grant READ permissions for Anonymous Users: yes
Choose "Save" at the bottom of the page.

Now the command:

curl --url http://host:8080/user/mr-c --user mr-c:${api_token}

produces this output:

HTTP ERROR 401

Problem accessing /user/mr-c. Reason:
Unexpected authentication type: org.acegisecurity.providers.UsernamePasswordAuthenticationToken@23fcf1a8: Username: mr-c; Password: [PROTECTED]; Authenticated: false; Details: org.acegisecurity.ui.WebAuthenticationDetails@ffffa64e: RemoteIpAddress: <masked for privacy>; SessionId: null; Not granted any authorities

This became a problem for me while trying to update my OS X slave using rhwood's jenkins-slave-osx script. I've filed a ticket there:
https://github.com/rhwood/jenkins-slave-osx/issues/33