I'm getting exactly the same problem on a 3-axis router. Did anyone ever figure out what the cause is? I get the flashing Abnormal Condition LED and "Axis not referenced normally" message. During Ref All Axes the light starts flashing when the first axis hits its Home switch. If I Ref any single axis on the Diagnostics screen, then switch to screen 1, I get the same LED. Double clicking it and asking Mach3 to redefine the state as normal turns the flashing off only until the next time I ref any axis.
Once today, I started Mach3 and didn't get the problem. The LED flashed while referencing all axes but stopped as soon as the last one was done. I hadn't knowingly changed anything. But since then the problem has come back.
My five inputs on LPT1 are separate Home inputs per axis, a shared Limit input for the other ends of the axes, and an EStop. I am quite sure they are all working and configured correctly, and can see no error on the Homing dialog or the Diagnostics screen. Indeed, it all seems to work correctly except for the flashing LED. I note that this LED is very new - it isn't shown on most of the video tutorials and doesn't seem to be documented.
Can anyone help, please?
Chris