What Java version are you running?
A possible reason for this problem I found is this Java Bug:
Bug ID: 4779905
Votes 35
Synopsis REGRESSION: If there are too many open files 1.4.1 deletes files
Category java:classes_io
Reported Against 1.4 , 1.4.1
Release Fixed 1.4.2
http://bugs.sun.com/bugdatabase/view...bug_id=4779905
Though I'm not sure if Phex runs against that limit...