What external hardware reset controller do you have on that board? What is driving PORESET?
If you don't have one, then that's the problem. These chips aren't reliable without an external controller. I'm meaning something like the Maxim MAX803 chips here/
If you do have one, then WHICH rail is it monitoring? How many power rails do you have? The CPU runs from the 3V3 rail, so that's what should be monitored, but if you have multiple rails than you might have a sequencing problem.
What other hardware do you have on the board, and is it all reset by the PORESET signal as well? Something else may be causing problems.
Do you have an external clock, and is it running after reset, or are you relying on the crystal on the CPU?
Put an oscilloscope on PORESET and HRESET and see what is different when it doesn't work.
You might have a similar problem to one I've had on the ColdFire chips. The problem is that the DRAM is on the Data pins, and so too are the gates or resistors that drive the data bus during reset to configure the CPU. When you reset the CPU on a power off, the DRAM controller can stop in the MIDDLE of a RAM Read with the DRAM driving the bus. And it KEEPS driving the bus and doesn't let go until it has been reset. This means the "Reset Configuration" doesn't work, and the CPU is now in the wrong mode, not generating a clock.. DRAM doesn't have a reset pin. The only way to reset it is to send the right commands through the DRAM controller, and in order to do that the Reset has to work and code has to have been read from the FLASH and so on.
A properly designed DRAM controller completes previous cycles on a reset and doesn't cause this problem. The ColdFire ones do have this problem, as well as generating "random" commands on power-up that can lock up the SDRAM. I don't know what the MPC860 does in this case, but you should monitor the reset lines, and the data lines to investigate this problem. If you do have this problem then pull-ups and/or pull-downs on the SDRAM Clock and Clock Enable pins can sometimes help to minimize, but not eliminate the problems.
Add some load resistors to the power rails to try and pull the 3V3 down to ground as fast as possible on a power off. That can sometimes help. Sometimes you need a power supply that guarantees to go all the way to ground on a power-off before coming on again.
> For some reason, this problem become more constant in the last produced boards
Have you changed your RAM chip brands or models recently?
Tom