Sorry if this is a bit vague, it's all off the top of my head. I'll have a dig for more info later.
Cold boot and reset aren't that different really
When resetting from the keyboard, the keyboard controller holds the reset line low for a short time.
There can delay this for upto 10secs if needed(eg when using a reset handler), but it can't cancel/stop a reboot.
When cold booting, the reset line is held low until the +5v supply has reached a set level. (Although if the 5v line goes below this point at anytime while the machine is up and running, it will hold /PWR_BAD and /RESET low until it stabilises again)
But on a reset, there can be things still resident in memory (patches/hacks/3.5 or 3.9 romupdates/virus) which can run before Workbench comes up.
So it might be worth checking what patches you've got installed in your user-startup or WBSStartup and run a virus scan to see if the problem goes away before digging out a multimeter.
Edit.
Have a look at
http://main.aminet.net/package.php?package=hard/hack/A1k2TReset.lha, for putting an external reset switch on the a1200, it should work every time,and is a lot easier than diagnosing a problem with the kb controller reset.