jenova_e.mov (disc 1) and ending2e.mov (disc 3).
The PSX always uses the new translation, and that includes new names.
It looks like the retranslated movies are the culprit. There's clearly something funky going on because IsoBuster can't extract the movies successfully even from the original, unpatched image.
I was able to get it sans-patched-movie by doing this:
To start, you will need a valid image of the disks where GG's patch applies successfully with no checksum errors. You should make a duplicate of each, because we're going to modify them and you want to keep the original in case something goes wrong.
1. Apply GG's patch and rename to beacause-1.bin, beacause-2.bin, and because-3.bin (for discs 1, 2, 3 respectively).
2. Extract /MOVIE/KERNEL.BIN and /MOVIE/SCENE.BIN from each of the beacause images. Name them kernel-1.bin and scene-1.bin for disk 1, etc. for remaining disks
3. Apply the FFVII Disk Extension Patch to the UNPATCHED bin file for each disk. Rename these to target-1.bin, target-2.bin, and target-3.bin respectively.
4. Use PSX-MODE2 to replace /MOVIE/KERNEL.BIN and /MOVIE/SCENE.BIN on the target image made in step #3 with the files extracted in step #2.
REM assumes kernel/scene files are named kernel-1.bin/scene-1.bin for disk 1, etc
ren kernel-1.bin kernel.bin
ren scene-1.bin scene.bin
psx-mode2 target-1.bin /MOVIE/KERNEL.BIN KERNEL.BIN
psx-mode2 target-1.bin /MOVIE/SCENE.BIN SCENE.BIN
ren kernel.bin kernel-1.bin
ren scene.bin scene-1.bin
REM increment all the '-1' to '-2' for disk 2, then '-3' for disk 3.
5. Rename the target-1.bin, target-2.bin, and target-3.bin to your liking, and rename/edit the corresponding CUE files to match.
Load up the CUE file in Mednafen and it should work.