[Michael Phelan]

Not sure if this will help but i had a similar issue caused by certain plugins. Gaussian blur and some transitions always caused a problem when rendered from progresssive to interlaced.
Again not sure if this helps but my solution was to insert a new video track on top,drop in a legacy text title, delete the default text but create an empty text space by clicing the space bar once.
Now you should have a blank text with an invisible space in it. Extend this title to the duration of your timeline.
When rendering the problem flickers are not created as the title text (blank with space) creates a buffer layer.
Works for me hope it helps your issue.