I've configured Merge options: Merge before build and entered a repository and branch to merge. Saving this config works OK, however each time I re-configure the job, I need to re-select this option and re-enter the repository and branch, because it is reset (Merge before build comes up unchecked). Saving the configuration causes the Merge before build to be turned off unless I remember to fill in the values again.
I have Jenkins 1.414 with Git plugin 1.1.9. Another server with 1.413 / 1.1.8 does not have this issue.