I can't reproduce this in my projects, although there's rarely going on really much on the screen, so it's not a perfect test. In any case, "context.clear" only takes up very little time there.
One more thing I forgot to mention: you have deactivated "Starling.enableErrorChecking", right? That's also something that has a very negative impact.
What I *did* see in the past is that I've got long "waiting for the GPU" spikes which I never could explain 100%. One reason they might happen is descried here — perhaps reading that (really interesting!) article gives you another idea what you could do to solve this.
And one more thing: you made some changes to your Starling version recently, if I remember correctly. Have you tried if this happens with "vanilla" Starling (head revision or v2.3), too? Just to be sure it's not an unexpected side effect.