Sounds as if you are losing communication with the BMDC. It is the biggest board plugged into your mother board. Pull it out (no need to pull the ribbon cables off but take note as to how they are plugged in just in case) and clean the edge connector with a soft eraser. Plug it back into the same ISA slot or another one, it does not matter.
With a machine of this age, check the logic power supply as well (voltage and fan). Check your CMOS settings. If the time and date are whacked out, your hard drive settings may be wrong as well. This would also mean the NICAD CMOS back up battery may be dead and leaking and may ruin your mother board.
Check your air filter on the control cabinet. A clogged one will not allow proper control cooling.
The executive is the BMDC.bin file. Do a scan disk and defrag after checking the CMOS. your hard drive may need to be nuked and reloaded.