merge vs. rebase question

As a git noob I am having trouble understanding when to use which commands. I have a repository (bare) on my Linux server. I also created a build directory as a local repository. In my build script I do a 'git pull' to make sure the build directory is up to date. No changes are made to my source so this repository never does an 'add' or 'commit'. When I run my script with 'pull', the output indicates that changes were found and seems to have pulled them into the local directory. However, when I look at the resulting source, none of the expected changes show up. I then tried a 'fetch' and 'rebase'. That worked but I don't understand why. I thought 'pull' did a 'fetch' and a 'merge' so I don't understand why a 'fetch' and 'rebase' worked but 'fetch' and 'merge' did not. Unless my understanding of what 'pull' does is wrong. In my case, what should I be using in my script to assure that the build directory is current?

Thanks.