Well, it looks like jagenc2.zip is the real deal.
I used it to "encrypt" the ROM image of Phase Zero and it passed the BIOS check with flying colors. Here are the steps I followed:
First, I stripped off the 8K of $FFs in front of the ROM image so that I was left with the raw binary image that loads/runs at $802000. Then, I put the PRIVATE.KEY on a floppy and ran the JAGENX.PRG (it's an ST program, and runs faster than the JAGEN.PRG version). It'll ask you if you want to use a precomputed key (which, if you haven't run JAGENX yet, won't exist) to which you'll say no. It will then ask for a floppy with PRIVATE.KEY on it. Once it reads the key, it will ask you which format to write out. Select option "1", 4 ROMs. Then it will ask you where the ROM image file is (you did put it on the ST hard disk, didn't you?
). Once you tell it where the ROM image file is, it goes to work crunching the data. Once this is over, you should have some files called FOO.U1, FOO.U2, FOO.U3 and FOO.U4 (where FOO is the name of the ROM image file). These files contain the "encrypted" ROM image with .U4 holding the Most significant bytes, .U3 holding the Next Most significant bytes, .U2 holding the Next Least significant bytes, and .U1 holding the Least significant bytes.
Combining .U1-4 into a regular ROM dump is left to the reader as an exercise.
One other thing: You'll want to run JAGENX.PRG in either medium or high resolution, otherwise you won't be able to see the whole text screen.