Codec packs, even the "better" ones, do not typically provide codecs that Premiere and Encore can use.
The "problem" file is a flash format (whether it is an mp4 container or not).
"Consumer" type DVD authoring/burning applications, and even more so, all in one apps like windows movie maker etc, may be more "powerful" when you are trying to take a large range of formats and create a DVD with relatively few options. This is not Encore's strength.
Encore will reject almost anything that has flaws it isn't able to handle, but more importantly (once you get to this step), it will treat as noncompliant (and re-transcode) anything that is not DVD compliant.
My guess is that you need to get the flash into something that will work better for transcoding to DVD compliant.
I would first try to bring one of the problem files into Adobe Media Encore, and see if you can export an MPEG2-DVD file.
Not that, while there are some less known DVD resolutions, I assume you are going to end up with 720x576 PAL. I wonder what the quality will look like....
If you are just looking to get the files onto a DVD to play on a DVD player, just stick with DVDStyler.