I often use Adobe Media Encoder to convert my videos to FLV or F4V for web, but end up with a 1 pixel green line down the right side. It's almost random when it shows up because it happens when I'm matching all the source attributes a lot of the time. Is it just a problem going from H.264 to Flash?

I have had the same sporadic issue even with just H.264 videos wrapped in an .MP4 file, so my guess is that it has something to do with the H.264 codec. What is the original format of the video or the sequence settings in Final Cut Pro? And can you post a screen grab of the image with the green line here in the forum?