Emulator

Game Name?
007: Nightfire (GameCube, USA)

Game ID? (right click the game in the game list, properties, info tab)
GO7E69

MD5 Hash? (right click the game in the game list, properties, info tab, MD5 Hash: Compute)
a824f5a7a553b7598592c6c129378262

What's the problem? Describe what went wrong.
While using frame advance, Dolphin drops most of the inputs in the menus for 007: Nightfire. It also drops inputs in the driving levels sometimes. The problem is easy to reproduce.

What steps will reproduce the problem?
The easiest way to test this is to enter the "codenames" menu and create a new codename. You are then taken to a screen where you type in a name. If you hover over any letter and press A every other frame, it will type in the letter once and ignore the rest of the inputs. If you do the following set of inputs (just as an example), you will reproduce the problem. Hover over a letter, then press A, right, A, right, A, right, A, right repeatedly. You will input the first letter and nothing else.

Is the issue present in the latest development version? For future reference, please also write down the version number of the latest development version.
This issue is present in the version I tested that was released a few days ago. The issue starts with version 5.0-5874. This update changed the way XFB behaves, which causes the problem for this game. Enabling "Immediately present XFB" in affected versions will fix the problem. Also, enabling "Virtual XFB" will create the problem in versions prior to 5.0-5874

Is the issue present in the latest stable version?

No. The issue is not present in Dolphin 5.0 unless "Virtual XFB" is enabled.

If the issue isn't present in the latest stable version, which is the first broken version? (You can find the first broken version by bisecting. Windows users can use the tool https://forums.dolphin-emu.org/Thread-green-notice-development-thread-unofficial-dolphin-bisection-tool-for-finding-broken-builds and anyone who is building Dolphin on their own can use git bisect.)

First broken version is 5.0-5874 unless "Immediately Present XFB" is enabled.

What are your PC specifications? (CPU, GPU, Operating System, more)

Windows 10 64-bit
Intel i5-4690k at 3.5 GHz
Nvidia Geforce GTX 1050ti
8GB DDR3 RAM

I have also tested this at a friend's house, and he has Windows 8.1, an AMD FX-8350 CPU, an AMD R9 270 GPU (i think), and 8GB of DDR3 RAM. The issue was the same on his computer as well.