I taped over the lights, she knew it was still "on" but suddenly, no headaches.
AIUI, there's lots of documented cases of flashing lights causing seizures (at least with people prone to them) and causing irritation and headaches in others. Perhaps, if they were in her visual range, they were of a colour, intensity and flashing frequency to cause her issues? Other colours, brightnesses or flash rates might not bother her.
On my Dell Latitude laptop I had to cover the WiFi light especially in low light, extremely annoying (HDD light was either on or off-but-occasional-flash for long periods, not the regular flashing of the other one). My last-ever Akai monitor has a bright red LED that slowly blinks when the computer shuts down. It sits between me and another screen and I have to yank the bloody power from it. Both give me migraines, but lots of other flashing/flickering lights aren't a problem.