I'm a bit confused here Phil. If you really want to cut on thin plywood then why are you burning on paper? Don't waste time burning on paper because it won't be the same (the settings that work on paper won't work on plywood). So, I'm not sure why you would want to troubleshoot burning on paper, even re-compiling new firmware, etc. when you're real target is thin plywood?
I burned on paper myself and found that really light power settings produced an uneven burn line. This is due to the paper surface finish. Light burn lines are difficult to do on any material. At this point I don't think there is anything wrong with your system, but some photos would help me to see excatly what you are talking about.
Unless you really want to burn on paper, move on to your thin plywood and please report on your progress.