Well.... yeah, it does.  Which mostly reflects my particular work style and environment rather than any rational design.  A number of people have complained about this in the past, but the reason that it hasn't been fixed yet is that it's somewhat difficult to avoid completely.  However, an update of Phenix for the bold new era of cloud computing is probably overdue; I'll see if I can deal with it this summer.  I should also mention, however, that when you have multi-user (or multi-computer) projects it is also difficult to prevent different instances of Phenix from conflicting.

-Nat