I have the exact same problem, to the point where yesterday I kept taking her off too.
Its not been too bad today but Ive been using loads of lansinoh on the nip - there was a slight crack to the top of the nipple.
I also have to latch DD on differently on the uncomfortable side, as the shape, size and position of my nipple is different.
I think its because I got a bit lazy with latching her on properly, that it caused some damage, and subsequent feeds hurt.
I also think that half way through the feed she comes off a bit, so I have to keep relatching her on again.
She also is a great cluster feeder, so when my milk production is a bit low, it hurts to feed on that side?
Anyway, enough of the rambling, hope the HV helps you :)