I'm trying to record Castlevania in FCEUX (emulator) but that little FPS counter in the corner doesn't show up when I have Fraps open.
I'm guessing the emulator can be played in windowed mode, therefore you could record your desktop and it should record the game too, then just crop the video
or adjusting your desktop resolution to something lower and then recording, saves a bunch of drive space and is easier on the system. Might still need to crop but not as much.
if anyone is still having this issue check and see if the emulator has an OpenGL or D3D output type. I've have no issue recording emulated games with FRAPS (everything from SNES9x, to Dolphin, to PCSX2, to DOSBox), as long as I was using an OpenGL or D3D renderer.