Another (intermittent) issue I noticed was when I was deploying a workspace to EA Server from command line. (Pb125.exe /w <workspace> /d ...). I am deploying PB15 to EAServer 5.5.
When I had an error, I killed the current and started again. Subsequent runs started complaining about "Null Password" against Oracle. When I checked the DB Profile in PB 12.5 IDE, the profiles were there, but the password was lost. At this point I couldn't even save the password and the default profile won't be checked. (I had these profiles set up earlier and they were working correctly before this happened).
It took me a couple of more tries to finally get the DB profiles back and the passwords magically re-appeared again, then the deploy process went OK.