I've noticed that the FMVs in Chrono Cross, Tenchu 2, and a few others in the HD Software video plugin is rendering two identical FMVs every time they come up at 2X Rez, and 4 at 4X Rez when using compressed disks from within the program.
When the video is over or skipped in Chrono Cross (Perhaps Tenchu 2 as well), the video becomes fullscreen for a mere moment before disappearing. This appears to be a plugin problem, but I can't be sure until I know how to send a bug report without the app crashing.
Additionally, resetting the games or BIOS crashes the emulator.