Interlacing issue with AME/Premiere CS5?

Hi,
I am having some issues with a file that I am trying to conform using AME CS5 from XDCAM-HD mxf wrapped to wmv output that I need to be able to playout of a black magic card to SDI.
The source file is 25fps PAL
If I import the mxf directly into AME (without going via Premiere), I can successfully output an interlaced file at 6Mbit CBR using the main profile and it plays out correctly on the monitor I am using to check playback.
However, I need to remove 2 channels of audio from the hires and overlay a logo. I have done this by importing the file into Premiere, making the necessary changes and exporting it to AME.
When I do this, if I chose interlaced as my output from AME the resultant file is terrible and movement is extremely jerky. If I change the output to deinterlaced I see an improvement but it is still not as good as the file that has been imported directly to AME without going via Premiere.
I need to understand (and resolve) what is happening within Premiere that is making a difference to the output file from AME.
Changing the output format to something other than wmv is not really an option at present.
I have tried changing the Interpret Footage settings in AME along with various other options. I appreciate that I may not have supplied enough information here for someone to be able to assist but if you let me know what else you need to know I will happily provide it.
Thanks

thanks for the clarification and apologies for the misunderstanding. I don't work in the video editing side of the industry so I'm not familiar with a lot of the lingo.
Unfortunately I have an absolute requirement to either use the prproj (or ideally the FCP xml option) output so that I can substitue the source media in the project and send multiple jobs to AME using an automated process.
I'm trying to understand what Premiere is doing to the hires file when it exports it that is causing the difference in the resulting output from AME when compared to submitting the hires directly to AME.
I'm just in the process of setting up a new project that only contains the hires, with no logo added, no settings changed and I am going to run that through AME using the same epr that I used on the direct import of the hires.

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