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I have been using Handbrake for about the past 5 years and I have library of over 1000 films now never had a problem with the quality and some of them are blurays ripped at 1080p.
Maybe you could post the specific issues you are having and what setting you are using and ill try help you with these.
When I batch did 300 last year, I used DVDFAB to rip (took 10/15mins to .VOB), then would leave handbrake running overnight to batch convert that day's rips (to mp4/m4v).