This is my source image. It's 8x8 pixels, 256 colours, the format Genitile says to prefer. The original is in bmp format but imgur seems to have formatted it to png.

Here's an enlarged version to see what it looks like.

My command line to convert it was this, pretty straightforward:
genitile.exe square256colors.bmp -sprw 1 -sprh 1 -o h
And here's what it looks like in Gens Rewind and Kega Fusion.

The top line winds up to be transparent, which is expected.
As you can see, the purple and yellow lines have been swapped around. Without seeing the source code, I can't really guess as to what's going on. I don't think the source has been released, has it?
IsaGenesis and Genitile seem both to be abandoned. Are there alternatives to these tools?
DJCC.