You run THREE batteries? Easy-peasy ... do the isolator thing ... you'll thank me later.

If all has been working previously, maybe your batteries are heading south. Cranking takes BIG amps ... if the bats aren't up to snuff, your voltages/amps will be doing crazy things while cranking. That plays hell with electronics. (Ummm, I'd have thought the battery connections would have been the FIRST thing you checked)