Hi Vishwa,
I have had some experience of PDMS bonding by plasma oxidation. Like you, I
tried a barrel etcher/cleaner and had no success with bonding. I moved to
an STS ICP system (which I think has a higher density plasma) 100W O2 for
10 secs and I have a 100% success rate every time.
With respect to your other concern, you should be able to tell if the plasma
has ignited by looking a the contact angles of your material post exposure.
If it has been exposed to the plasma your contact angle of water will
dramatically reduce.
hope this helps,
Paul