I would try flashing the BIOS on one machine to see if it stops the problem. (Make sure the test machine has no HDD in it when flashing, and a new or freshly wiped* HDD installed after.)
You may have to replace the BIOS chips, or have them fixed by experts.
If this malware is as sophisticated as you suggest, it may hide in any firmware attached to the system. It may also survive flashing the BIOS. If you know exactly what the malware is (name, etc.), you can find a better, more focused way to fight it - look it up, or contact experts.
If you are not positive it is BIOS or firmware malcode, try wiping* the HDD and reinstalling the OS.
Wipe - mean forensically scrub the drive so nothing survives. A format does not do this. DBAN and Killdisk are free tools to do this.