So you run SC from CLI and it works and on SAME maching call same command through SMVI and it doesnt?
[Fri Nov 9 12:04:57 2012] [126.96.36.199:9090(188.8.131.52)] ERROR: [scf-00139] Application quiesce for plugin db2 failed, no exit code returned from plug-in, Exiting!
Means that the SC server got back no exit code from plugin, basically the plugin returned a response with no messages or exit code. Usually this is some kind of communications issue between server and agent.
Something has to be different, I would focus on what is set when things work and not set when it doesnt.
You can use "set" to print all the ENV parameters, maybe SMVI is setting something or something isnt set which is when things work. I would look at this.
Let me know if you get any further in troubleshooting?