Emulator

Can confirm this happens as well.

Happens with me as well, but isn't it well-known that Rogue Leader and Rebel Strike have lots of issues right now since they're still only recently able to be emulated?

It's important regardless.

The transitions happen if you use RealXFB.

I had tested that, as I had initially thought the same thing, but it's not true. Just retested to make sure, same issue is seen regardless of XFB setting.

This bug doesn't actually capture what the issue actually is. What's going on is that on the original hardware, there's a fade to black after the movies play that fades back in to gameplay very quickly. What happens on Dolphin is that this fade to black isn't emulated, so the game awkwardly moves the video over a bit before switching to the gameplay - a transition that is hidden by the fade to black on the original hardware.

The YouTube video in the original report shows what happens with the game on the original hardware. The YT vid I'm about to link show the same scene running on Dolphin, albeit an older version - pay attention to what happens after the video finishes at around the 2:00 mark:
https://www.youtube.com/watch?v=YFzlTM-6AvE

I don't have Rogue Leader to test against newer builds, but I do have a game that has a similar problem - Soulcalibur II makes use of these fade-to-black transitions as well for switching scenes but because Dolphin can't emulate them, the transitions are awkward jump cuts to a new scene instead. I previously filed a bug for Soulcalibur II's lack of fades at Issue:8429, but there hasn't been much movement on that bug there since the switch to the new issue tracker. I can confirm these issues still happen on SCII on build 4.0-9308, and it happens regardless of the XFB setting.

That's true, Dolphin is missing some kind of fade in a lot of games.

From Julian Eggebrecht:

The video is a additive alpha layer over the background. The video itself is mjpeg.

This worsened a bit with Hybrid XFB, as the transitions now render as bright purple. Requires XFB to Texture disabled to render appropriately.

that's not any worse? They rendered bright green before in RS3