Here's one of the many streams, most sup's I've converted to 720p with BD-RB has shown the problem so I think it would be a pretty common issue. I just found BDSup2Sub earlier today so this is the first.
I think it is issues with the streams like you say, I've seen many strange displays with SupRip over the past year or so but they seemed to ocr ok so I didn't pay much attention to it. But these strange displays play fine in the retail somehow.