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PS: support can only help if you upload logs https://www.veeam.com/kb1832
Rovshan Pashayev
Analyst
Veeam Agent for Linux, Mac, AIX & Solaris
I since found out that this only happens to lvm based linux systems, when veeam tries to add more than 1 disk to the vm boot order. I'm going to work with support on resolving the case and will post here again if we found the issue.
Turns out the current PVE Plugin is using the wrong delimiter when adding multiple disks to the boot order. Veeam provided a fix to me which solved this issue.