1. I enabled Active Directory Plugin
2. I enabled Project-based Matrix Authorization Strategy
3. I gave some users access to log into Jenkins and also give them access to view/build jobs
4. For one of the users, his login name in Jenkins was in uppercase
5. The user with the uppercase name was able to log into Jenkins
6. However, the user was not able to see any jobs that he was given access to build

To Fix

1. I went into the job configuration and under "Enable project-based security" I remove the uppercase username from the job
2. I added the user again, this time making the username lowercase and assign the same permission as before to the user
3. The user logged in and was able to see and build the job

Seems like a case-sensitivity issue to me...