Trouble with start up

With my Tormach PCNC 1100 the start up is computer first then machine . At this point the red LED at the top position lights up , then you hit reset and the lower red LED lights up . Now comes my problem , somehow I have gotten this out of synch . I have tried to clear this up but do not seem to to be able to trouble shoot the problem . Is there anyone here who would care to set me straight ?

Many thanks in advance ,
ErnieD