Solved this, started thinking it might be caused by the last app I installed, so had a look at my tce/onboot.lst file and the last app I installed as firmware.tcz
I installed this as I used to get following error during boot up.
Feb 26 03:06:41 (none) user.err kernel: eth0: Failed to load firmware "tigon/tg3_tso5.bin"
Did some looking around the tinycore forum and discovered post about this error with suggestion to installed firmware.tcz which contains tigon/tg3_tso5.bin among others.
So I did
tce-audit builddb
tce-audit delete firmware
sudo reboot
Have done a few shutdowns and reboots and the shutdown crash has stopped. I get the tigon/tg3_tso5 error on boot up now, but its harmless and does not effect normal operation of the server.