lerameur, Joe S. is right.... I have been designing test systems for about 30 years and have repaired problems with systems that stemed from having multiple grounds. If I was to design the type of system you are talking about I would have 1 single ground point. The noise you are talking about (upsetting the processor) is more than likley caused by the current being drawn from the 24 volt return from the motor drive system and where you are sensing or referencing the ground. I can't beleive that the processor 12 volt supply is that noisy or is drawing that much current. If both battery system returns were tied together at the batterys this should eliminate most of your problems. How much current is the 24 volt motor supply battery required to deliver?

Dave Purola,
N8NTA