Hello,
What you have observed is suggestive that "latch-up" of the MCU might have occurred, where the MCU becomes continuously short circuited until power is removed. The MCU will generally suffer permanent damage.
The most likely cause of this condition is that the "injection" current into one or more of the MCU pins has exceeded the specifed limits, which only need be for a few microseconds. This can be caused by an external voltage surge, maybe due to a nearby lightning strike, or even by static discharge from the human body. The design of the interface needs to isolate the MCU from these potential surges of up to "a few thousand" volts.
For the MC9S08JM60 device, the USB port interface may need some attention in this respect. Perhaps the MCU has an independent grounding arrangement from the USB host, allowing transient surges to occur between the two grounding systems, and find their way to the MCU pins.
Regards,
Mac