I'm just following up on an old BorisRED4 problem that I had with Media100HD 11.5.1.
To briefly recap, if I tried to alter video from the timeline in a title or composition clip placed upon it, that altered layer would render out as black. Everything else (logos, text, overlays, etc) would be ok.
Now that I have RED4.1 installed and unlocked, this bug appears to be squashed! This morning, I've been doing some heavier multi-layer work with it and there's no unwanted black in sight.
I can address this with my aging experience. Since you are working with title clips, make sure there is no unsused text layer at the bottom of your comp, as one usually made automatically when you select grfx. I have found it you don't use it, the black thing happens. Perhaps this applies to you.