The interleaved file is interpreted and exported correctly, so there is no need to import each discrete channel. I downloaded Audacity and the FFMpeg plugin to check the ac3 channels and they where identical to the original exept for minor overall level differences which seemed to be the result of a normalization of the channels – but that has to do with the DD 5.1 settings in the Inspector window.
Another major issue I dealt with was that I had made some minor cuts in the interleaved file while editing in Premiere so in order to have the video file and sound file exactly the same length in Encore I had to export it from Premiere in order to open it in compressor. I managed to do so by changing the channel settings from Stereo to 5.1 and exporting as an uncompressed 5.1 wav file. Neither the AIFF nor Quicktime codecs managed to export 5.1 without deleting some channels and ruining the surround. Don’t know why that is.