I'm fairly new to Boris Red (4.3 with FCP 6.0.5). Actually this is the first time I've really done anything with it. I was really intrigued by the idea of custom transitions so I thought I'd give it a go. So everything went fine with creating the transition from FCP>Boris and when I applied it the transition worked on the video just fine, but the background behind my 16:9 footage disappeared for the duration of the transition then came back afterwards. I can see that the glow of my transition goes beyond the bounds of my 16:9 footage so is Boris automatically filling my 4:3 frame with black? Is there a way to turn this off? Sorry if this is an extremely basic question, but I couldn't find any posts that directly addressed this problem.
It may be that you have a layer in RED that is obscuring the background video track. Please feel free to send me the RED project file and I'll take a look at it. If you send along the RED project file, please include a screenshot of the FCP timeline so that I can see what video tracks are in the timeline that would help too. You can send that to me at email@example.com.