I don't know vidcoder (which itself is apparently a handbrake frontend, and handbrake is mostly a collection of other tools) enough to say, and removing noise from things is always a fun one (especially trying to do something generic across a whole video, to say nothing of the issue of reencoding multiple times presumably to lossy each time) which I like to play by video, or indeed by scene.
You can try real time removal. Most of them work about as well as the basic attempts which most such programs go in for.
Why do your sources have so much grain anyway?