Compressor for JVC files, good work takes time?

Hi,
I am using Compressor to convert my JVC footage (*.TOD, 1080P output) into ProRes 422 (HQ) before importing into FCP 7 (being "native" to FCP). Trying to keep the quality maximal.
Up to now I found no other way than to first convert to h264 *.MOV (for which PavTube TOD Converter gave me much better results than MPEG Streamclip, but maybe I got lost between those millions of settings). Then I use Compressor 3.5 to further convert to ProRes. Files have been compressed first (about one third of original size), but during the Compressor process they get decompressed again (about ten times). Wonder if I loose a lot of quality in the process?
Besides, Compressor is taking forever to do the job. Once the batch is running, it is relatively fast (multithreading is still another age), compared to preparation of the batch, even on low priority. Dropping more than ten files onto the droplet makes it stop responding for 15 minutes, then submitting takes another five. Is there a better way to make the process smooth and quality preserving?
Has any of you experienced users a clue for me? I would be very grateful, meanwhile I keep crawling on with my superfast Mac.

Hi Zak,
Sorry for not coming back before, I was away for some time. Thanks for your answer. I tried very many settings in MPEG Streamclip, but most interesting will be to set up both MPEG Streamclip and PAVTube TOD Converter with the same settings. I took a clip of a Newspaper page plus fast movement of the camera, full daylight.
MPEG Streamclip:
1. Codec h.264, Qual 100%, B-frames, rate 25, Size 1920x1080 (16:9), Interlaced scaling, Reinterlace Chroma, Upper field first, then
2. Codec Apple PrpRes 422 (HQ) other settings same (except B-frames, greyed oput), then
3. Codec XDCAM EX 1080i50, B-frames, frame rate 50, others same
versus PAVTube TOD Converter
4. Codec h264 HD Video, 1920x1080, Rate 12000, frames 25, audio aac, 48 kHz, Bitrate 320000, Channels 2
Results:
1. Sharp, but interlace lines visible, motion blur
2. Sharp, but interlace lines visible, motion blur less
3. Less sharp, no interlace lines visible, motion blur
4. Sharp, no interlace lines visible, motion blur less.
It is clear to me, that 4. gives the better results. Be my guest to repeat the experiment, you can download a fully functional copy of PAVTube on http://www.pavtube.com/tod-converter-mac/ Only thing is a watermark in your output.
Please advise me if there are any flaws in my approach, I will be grateful for suggestions how to get (even) better results.
Re Compressor, it does its job well, but why the long waits, there must be smart programmers with Apple who can do better, or am I doing something wrong? I use a droplet which starts the program by itself. But twice submission plus waiting takes an hour for a complete folder of some 1,5GB of clips.

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