This problem probably needs a bit of explanation.
1.) The test4theory project (aka LHC@home 2) is a bit special: it runs its task in a virtualbox VM.
2.) The boinc startup script runs boinc_client using su -m, preserving root's enviroment but running as a different user (boinc by default).
These two settings are incompatible: VBox needs a proper $HOME, but gets the inaccessible /root instead.
A usable workaround atm is to replace "su -m " by "su - " in /etc/init.d/boinc. You may also need to set 'usermod -d /var/lib/boinc boinc' (or whatever your boinc RUNTIMEDIR variable is) if you haven't done so already.
Hint for Test4Theory users: unless you are running boinc_client as your desktop user, you also need to make sure that you enable headless mode in the project specific settings.
I'm unsure how to properly fix this atm, for two reasons:
1) I don't know the reason for su -m.
2) According to forums, some users run boinc as their desktop user, so they might want $HOME and $RUNTIMEDIR to be different (this will still only work with test4theory when using su without -m)
The current ebuilds no longer use the su command directly and the daemon should be fine again with virtual box.