Do you mean that enabling pdf-a in V3 would solve the color problem?
No. It just removes some transparency things to make the output compatible with pdf archive standard. So that won't help
I discovered the problem on our old production server with jsreport 2.11.
I see, v2 doesn't do anything with the colors. It's the output from chrome. I've never noticed this problem. Try to isolate the problem. Put just the image to a template, does it produce bad output? Try it locally. The same?