Well, figured it out.
It was the Y limit switch.... why it ties into that particular line I have NO idea. It makes no sense, but that's what it is.
The EMG override is just a toggle switch that temporarily allows axis movement even when the machine is on the limit switch... we did have problems with the Y limit switch before, where it's located, it tends to occasionally get a splash of coolant on it... this dries and turns gummy... and happens over and over, making the switch "sticky". So I think the reason the error disappears after a while is that once I move the table off the switch, it eventually pops back to it's non-tripped state on it's own, which kicks the control out of the error code.
Strange, but true.
I'm not sure how the other axes are tied in - for all I know, they would produce the same error code, probably do actually.
Thanks for the help!