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Can you expand more of what you mean when you say "the branches on our build boxes aren't updated"?
When I define a job with the git plugin, I define "branches to build" as "*/master". Once I've done that, then any changes I submit to the master branch on the central repository are detected, pulled into the Jenkins job repository, and built. Those changes appear in the list as "recent changes" and are used by the build.
A "merge" is not shown in the Jenkins build log because no merge is needed. The plugin checks out the tip of the branch "origin/master" by SHA1 and thus does not need to perform a merge (in that case).
The plugin can be configured to perform a merge, but usually that is a merge from some other branch to the current branch, not a merge from origin/master to master.
If you want to merge multiple branches before build, there is an "Additional Behaviour" "Merge before build". It's help says "These options allow you to perform a merge to a particular branch before building. For example, you could specify an integration branch to be built, and to merge to master. In this scenario, on every change of integration, Jenkins will perform a merge with the master branch, and try to perform a build if the merge is successful. It then may push the merge back to the remote repository if the Git Push post-build action is selected."