Maybe it hurts to suck and swallow because of her ear infection.
I was going to suggest that too. Ear infections really hurt. I know when Natty's ears were infected it was the sickest she'd ever been. Are you giving her panadol? My Dr told me to keep it up four-hourly because the discomfort is really quite significant.
Poor little one (and you and your DH with the flu at the same time! AAgh!). Hope she's feeling much better soon. I'm sure she'll be back onto her milk once the worst of the infection has passed.