Hi Lukasz,
May I ask which version of Veeam Agents do you use?
Recently we have
thread with similar issues maybe discussion there will be helpful.
The first time the job is launched, a folder with the backup will be created. But if such a folder already exists, then the backup will be created in the <folder>_1 (and so on)
So if you have several jobs with the same name for different Window PC, it can cause such behavior, as folder already exists.