The only thing I can suggest is maybe trying to pat her to sleep IN her cot as I found my DS would wake the minute I tried to put him in the cot asleep too!
We have turned his cot into a toddler bed now and put it right next to our bed (he used to co-sleep) and I pat his back to get him to sleep most nights. I still BF him to sleep sometimes as well but am trying to stop it as I have another bub coming soon.
I hope things get better soon x