I have a timeline that I wanted to convert from 1080i to 720p. It also contains one clip that requires motion stabilization. I applied a stabilization effect to that clip and it worked fine. Then I added Fluid Film progressive to all clips (nesting it into the clip with motion stab). I converted the sequence to 720p and rendered the timeline. All the clips lost their interlacing and the one with stabiliation came out solid. It played perfectly in Avid and looked great. I exported the video tracks as a Quicktime DNxHD110 720p file. That export plays fine in Quicktime - no interlacing and the motion stabilization looks great. So now I have a fresh clip, one piece, in Quicktime, that looks just the way I want it.

Then I imported that Quicktime file into into Avid and edited it into a new sequence where titles etc. and audio were added. I also did a few add edits to cc several sections. I rendered that timeline. It plays fine in Avid. Everything looks great so far.

Now the problem: I exported the final sequence to QuickTime DNxHD. But now I have lost the motion stabilization. Also, that clip and a few others have gained back interlacing lines. How can this be possble? The video is now just a single track made from the rendered Quicktime file that looked fine. It doesn't make any sense but I have gone over this several times, re-imported and exported etc., and the final DNxHD file still is missing some effects.  I have triple-checked to make sure I am rendering the correct sequence and it comes out the same way every time. My project format is still 720p and my sequence is 720p according to the bin description.

How can effects be missing when they have been rendered in and made into a new Quicktime file???

That doesn't make sense to me, either.  Why don't you try a video mixdown of your sequence and see what happens?