Ok - now this is even more interesting.
After I tried adding the files to Encore I realized I was working with a 1080p @ 29.97 fps file, and Compressor had encoded the video stream as such. The problem is that blu-ray doesn't support 1080p@29.97, only 1080i@29.97, so I re-encoded the stream with upper field first.
Still, Toast wouldn't touch it. MEPG-2, Blu-ray usage, 30 MBps, 35 Max and Toast multiplexed part of it and then decided to re-encode it.
Gave it to Encore - no problem.
Safe to say - something in how Compressor encodes MPEG-2 Toast doesn't like.