It sounds like you have run into the PR/460909 caveat. JUNOS release 9.3S6, 9.5S4.1, and 9.6S2.1 are the latest releases for the 9.3, 9.5 and 9.6 trains respectively as of this posting. I hope included references are helpful.
The first publication that I noticed the PR/460909 caveat being published was PSN-2009-07-461.
References:
PR/460909 Commit failed because rotation of configuration files to /var/db/config failed
Committed in JUNOS 9.3R4; 9.4R4; 9.5R3; 9.6R2; 10.0R1
PSN-2009-07-461 JUNOS Service Release Service Release 9.3S4.1 for the EX-Series Switch service impacted issues resolved.
PSN-2009-12-598 JUNOS Service Release 9.3S6 for the EX-series Switch service impacted issues resolved.
PSN-2009-12-600 JUNOS Service Release 9.5S4.1 for EX-Series Switch service impacting issues resolved.
PSN-2009-11-581 JUNOS Service Release 9.6S2.1 for EX-Series Switch service impacting issues resolved.