Your FI has some in built troubleshooting intelligence to enable your average dealer to find out what the problems are.Part of this is to make the FI lamp flash when there is a 'failure' of either the input sensors,fuel injectors or the ign coils.
Whats happening is that the FI computer is sensing that your coils are going awol(when the +12v is removed) and is telling you so by flashing the light.
Some people overcome this problem by bringing the shift kill time down to be as short as poss or by killing the FI pump or by switching the drive to the light off.Whilst all work I think the best way is to trick the FI computer into thinking that the coils are still there on the ign kill, this way the FI computer can go about it's daily business thinking all is ok.
I make such a device but I believe there is also some USA based maunfacturers MPS maybe Motorhead knows?
GASABUSA