Whoa, whoa, whoa.....what is with this misinformation???
1) What is the EvoX D.6 BIOS going to do that the X2 4976.02 won't? Nothing. It is aged and has no advantages over the X2 BIOSes.
2) No EvoX BIOSes have IGR built-in to date. Not D.6. None.
3) The "Matrix Inside" is just a LogoX hack on the evoxdash.xbe file. It is not in the BIOS. So far Team Xecutor is the only team to have edited the logo text within the BIOS itself.
That being said, it is FAR more likely that you're experiencing an alignment problem than a bad flash. You were fine with 4976.02 on there the first time. If you intend on using that as your primary BIOS, you may as well reflash the chip with that to get it out of the way. Once that is done, work on your alignment some more. If you're getting the 3x-restart and the frag, you know your d0 is fine. As you had said make sure your LPC points are aligned correctly.