I've noticed that I've been experiencing a rather unusual buildup of Passphrase temporary files building up in my /tmp filesystem - about 1.3 million to be precise. Some initial investigation suggested by @epriestley, namely P1040 (the test tmp file was deleted on my system) and P1041 (did not stop the behavior).
Starting the phd daemons in verbose/trace mode yielded no apparently useful debug.
After randomly flipping switches like a rabid monkey, I have observed that disabling tracking of an externally hosted subversion repository appears to have cause this behavior to cease in my Phabricator install.