Poor transition quality

Hi there, I posted this on the Compressor section in error as I think it is more of a FCP query, so here goes.
I am just completing an HDV job for delivery as SD DVD. I captured and edited using ProRes 422.
Most of the job has encoded fine using Export to compressor, best 120mins (job is 101 mins total).
I have however noticed two problem areas. both involving transitions, where the quality is very poor.
One in particular maybe challenging as it is a slow cross dissolve from a night shot into a very misty dawn.
I am trying to get that lovely transition of time from night into a gradual misty early morning, but at the moment it just looks a mess. The movement of the mist looks really pixellated and grainy. The footage without the transition is fine.
Do I have to do something special with these clips independently, like export them and encode at a higher bitrate and re import? or am I making it difficult for myself?
I am just not sure how to improve the quality if the current transition looks rubbish
Any advice would be appreciated
Thanks
Stuart

When you export your reference file for use in Compressor, make sure you check Markers>DVD Studio Pro Markers. This should give chapter and compression markers where ever there's a cut/transition.

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Thank you for the reply!
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