As part of the branch I have had to assign a particular range for label id's in one of the branches. This is to avoid conflicts when merging the label files. You set up the label id range from Version Control / System settings / General. Changing this, triggers a change to VCSDef.xml which is also under version in TFS.
This is obviously not a change that I'd ever want to merge. Fortunately there is a way to tell TFS to discard the change when suggesting what to merge. There is no UI for the command, so open a Visual Studio command prompt from the workspace folder to use and enter the following:
tf merge /discard /version:C1134 /recursive SourceBranchName TargetBranchName
This also triggers a change, so you must check that change in. And that's it. The changeset is not suggested for merge between these branches again.