I'm having a somewhat similar problem as pacinimac, although my modded xbox has only been running for 2 weeks, not 8 months. I have a v1.0, thomson drive, 160gb HDD, and xenium chip, but I have been using the 4981.06 bios.
Normally, the bios boots correctly, however, occasionally I get a 3x reset and a FRAG. After a frag, I have found that the only way to get the bios to boot again is by running an original xbox game off of the original MS bios, then powering off and rebooting. This fixes the problem momentarilly, but after several hours with the xbox off, it will want to frag again. It is quite annoying, so i'm trying to fix the problem, even though i can easily get around it by booting an original xbox game. I think it may be something with the xbox clock settings, as every time I go into MSdash it asks me to reset the clock. And this would make sense, considering the bios only decides not to boot if the xbox has been off for several hours. But I don't understand why incorrect clock settings would keep the bios from booting correctly.
Pacinamac also mentioned installing ninja gaiden, which i have also done recently. I have been unable to get it working, but i have found that it requires some type of media patch in order to play. But that's besides the point, I don't see how installing ninja gaiden could conflict with anything about how the bios operates, but i'm no expert so I don't really know.
I don't thing i have a loose d0 point, but i can't say for sure.
Most likely there is some conflict between MSdash clock settings and my dashboard clock settings (Avalaunch is default dash, Evox is secondary, both boot w/ 4981.06 bios). I don't understand why it would prevent the bios from booting though.
I'll try playing with the dash settings, but I don't know if/why it would help.