When you said that did you mean just fast flashing red or did you mean flashing red then green?
With the led set to green solid (0x408f = 0x19) try setting 0x409B to 0x10. It should make the led flash slowly (about 1Hz) but it may be between green and (some other state!).
OT: ISA, amazing! I think the only time I ever had anything to do with ISA was when I tried to upgrade my (then modern!) 386.
But I digress. What I meant by the same but ted was that the led flashed as fast as when it was green, but that it was the red led that was flashing.
So just red flashing.
./writeio 0x409B 0x10 results in slow (1 second/Hz) flashing, alternating between red and green (as you thought it might).
To iterate what we've found so far:
./writeio 0x408f 0x11 - turns the led green and blinks (fast)
./writeio 0x408f 0x03 - turns the led red and blinks (fast)
./writeio 0x408f 19 - turns the led green without blinking
./writeio 0x409B 0x10 - turns the led green and blinks (slowly)
./writeio 0x0408f 0x09 - turns the led red without blinking
Is that correct?
And does this give us the means to control the led completely, or is there something else that we need to test?