I would be very interested in any answers to this question. I have had the same problem with HDV captures (from FX1) One long (1 hour) scene with no stopping of the camera during thst time. When captured Vegas breaks it into 5 different scenes of varying lengths.
I do not have FAT32 drives
I am capturing via firewire
I also lose a small amount of the video between scenes.
I am capturing to separte drives from the OS.
I think that if you set up your project settings at 4:3 and drop your 16:9 footage on itand then use conform to project settings (or whatever the wording is) you can use it. You might have to use track motion to move the part of the 16:9 image you want visible into the field.
When you make the PiP at the event level and place the Sony Border fx on it and the fx window pops up look to the left of the word ‘border’ on the keyframe controller. There is a little arrow head. If that points to the right it will place the border around the entire scene. However if you click on it it will change and point to the left andf the border will be only around the PiP. I think it controls “before or after processing”