I had the same problem with my 1st. He would wake up as soon as his head hit the crib. I finally figured out that the crib sheet felt cold to his head, and that was what was waking him up. I switched to flannel crib sheets, and had a much better success rate :)
Before you run out and buy some, you can check to see if that is what is waking your baby by getting a fleece blanket and covering the crib sheet with it before you put her for a nap. It should be long enough to be able to tuck it tight and under the mattress. I am assuming also that your baby is too little to roll around much, and therefore there wouldn't be any danger that it could come untucked. Try it for one nap and see what happens.
If that's not it, maybe she startles going from a verticle position to a horizontal one. Maybe lay her in your arms to get her used to the position for a little bit 1st, then try to move her.
It could be that you just have a really sensitive baby- you mentioned she sometimes wakes when you take a deep breath. Again, I don't know how old she is, but at some point (about 3 mo old) you should be putting her in the crib when she's drowsy, but not asleep because she needs to be able to fall asleep on her own. Don't do what I did with my first and get her used to falling asleep by being held or rocked- it never ends :/ My first didn't sleep through the night until he was 2.5!!! With my 2nd, 3rd, and 4th, I put them down when they were still awake, and they were much better sleepers :)
Very best wishes!! :)