Apparently something is screwing up the flashROM. Afik there are no viruses around who would do this. Maybe the flashROM is worn-out (they do last long but not forever).
A few really old viruses erased the flash chip (CIH virus), and in theory it would be possible for a virus to corrupt only a part of the flash chip, but I don't think this happens here.
Sometimes even brand new flash chips have some stuck bits, and it is entirely possible that this happened to you. Depending on the board, there may be a jumper which causes the BIOS to reset ESCD before reading it. That could help. If you decide to reflash with an external programmer again, please make a backup of the current flash chip contents. It will be interesting to compare it with the BIOS image you flashed back when you recovered the first time. If only the ESCD region is changed, then there is probably some ESCD corruption. If other areas are changed and only single bits changed there, the flash chip is probably too flaky to be used.
Side note: If you don't know how to analyze the BIOS chip changes in detail, tell me and I can take a look. I've been active in various flash chip projects and this looks like a fun analysis.