For the records, I came with these problems again.
I had several instances of VBoxSVC, so I lsof them, and found that the one started with vagrant has permission denied to some files. I have had downloaded the packed version of the vagrant binary and it seems to uncompress itself in the /tmp directory to be run. This seems to create kind of a virtual environment for vagrant to run, but this environment then also applies to virtualbox clients (VBoxManage), making the VBoxSVC not to run properly.
As I installed vagrant from source, problem was solved.