Mixing Progressive & Interlaced = confusion

I'm working on a project where half the footage was shot Interlaced with a Sony camcorder and the other half progressive on a Canon 7D.
I've done some testing in FCP 6 using an interlaced (field domiance set to upper) sequence and a progressive (field dominace set to none) sequence and inserting one of each clip. Both look fine until I apply a 50% speed reduction (which I will do a fair bit in this project). On each sequence the non native clip looks jittery when motion is slowed down.
The best result I had was using the interlaced sequence and applying a deinterlace filer to the progressive footage. It doesn't make sense to me but it removes the jittery motion and looks cleanest (on my imac monitor). Still I'm confused as to whether this is the best path to take or if I should be trying other stuff.
Clip specs
Sony size: 1440 x 1090,  fps: 25, compressor: HDV 1080i50, Field Dominance: Upper
7D size: 1920x1080,  fps: 25, compressor: Apple ProRes 422, Field Dominance: None 
Suggetions/advice appreciated. 

Try sending the speed changes to motion and making them optical flow.  Much better results than within fcp.

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    Tagged date                      : UTC 2014-09-15 23:21:35
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    Format                           : AVC
    Format/Info                      : Advanced Video Codec
    Format profile                   : [email protected]
    Format settings, CABAC           : No
    Format settings, ReFrames        : 3 frames
    Codec ID                         : avc1
    Codec ID/Info                    : Advanced Video Coding
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    Width                            : 1 152 pixels
    Height                           : 720 pixels
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    Format                           : AAC
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    Codec ID                         : 40
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    Bit rate                         : 125 Kbps
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    Channel positions                : Front: L R
    Sampling rate                    : 44.1 KHz
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