Comment # 3 on bug 1156421 from Franck Bui

(In reply to Fabian Vogt from comment #1)
> Here it switched to /var successfully. So the question is why it does not
> happen (reliably?) when running during boot?

Hmm... the only reason I can see is that /var is still a RO partition at the
time the journal is flushed and therefore the system journal couldn't be
created in /var.

But you would get an explicit error on the next reboot since this time the
journal file was already created when you flushed the journal manually and
journald would fail at opening it RW.

Can you see such error ?