I have had the black frames issues with footage shot, edited and graded in 29.97. The problem usually happens with 1080i material but not with 525i. Anything in 23.98 works fine. The black frames only appear when doing the round trip from Color to FCP. It happens randomly through out a sequence and they are only 2 black frames at the end of edits. In a sequence about 45min long with 1500 edits (TV) we probably encounter 15 - 25 of these two black frames.
The weird part is that just last week we decided to do renders in another system with the same exact configuration. The only difference is a 2010 Mac as opposed to a 2008. The black frames never appeared in the 2010. We were under a super-tight deadline so I didn't want to start looking into it then but this week I will.
One thing that comes to mind is maybe there is a piece of software that the 2010 does not have that it is in the 2008. Other than that I am clueless. If that is not the problem, I'll be very surprised if the difference ends up being how old or new the Macpro is.
Stuart Ferreyra Timecode Multimedia
Colorist / Post Supervisor
West Los Angeles, CA