You are correct looks like all jobs are operated by the same, and yes backup copy job can`t use same repository as source and destination.
Workaround is to create any new folder on the same physical repository, add new backup repository pointed to this folder and then use it in your jobs configuration. In this case you will have the same physical repository, but Veeam will treat it as two different logical repositories.
FYI, v9 has a new component, called Backup & Replication Console
which can help decrease number of backup servers used.