Thanks Stan
Yes, it is the Encore to Flash export I'm talking about.
What I did was export F4V files from Premiere using one of the presets, no changes at all.
I tried a few variations, as well as varying the default project settings on opening Encore.
I brought these F4Vs Encore, but Encore insisted on transcoding the flash assets when I did the flash export.
I think the answer is going to be to bring in a high quality lightly or uncompressed asset and let Encore do its own encoding.