Intel Rapid Start (IRS) is mainly a software component with interaction with the BIOS. How it works is, IRS determines what exactly is necessary to run Windows and what isn't. Whatever isn't necessary, IRS flushes from the RAM, reducing the amount of data stored in the RAM. IRS then puts the computer into "Sleep" mode. The RAM still needs to be powered on at this stage. While in Sleep, IRS copies the data from the RAM to the SSD and then the system enters hibernation mode, requiring no power usage whatsoever.
The problem occurs, to prevent your car battery from draining, the M4-ATX will perform a hard power cut off after 1 minute. At this stage, the computer still needs to be left powered on for a bit longer. When the M4-ATX shuts the power off, the computer is still in sleep and has not entered hibernation.
Two choices to fix really. First option and would be the best, is force IRS to enter hibernation straight away somehow through software.
Second option, increase the duration of time the M4-ATX will continue to supply power to peripherals, therefore allowing the system to enter hibernation. This isn't a preferred option as it can drain your car battery, giving you problems!