The most likely reason for the bitch's behaviour is that you are too close and are threatening to her. The fact that the bitch is very quick to get your scent off puppies that you have handled, is agressive to others in a random, to you, pattern and seems generally uneasy says to me, "Back off!"
Leave her alone. She knows what she should be doing and you are confusing her. She has deep maternal instincts that are in conflict with her submission to you. Give her a two to three day respite where you only look in, not touch any puppy, to see that all is well and let her out to toilet. Then start to go into the whelping space only to fuss her for one day. The next day you only need to put your hand on the pups, not pick them up, take your cues from the bitch. If you respect her instincts in this it should not be an issue and by the time the serious socialisation time for the pups is here you won't have a problem. Do not force yourself on her, she will be confused and the only way to deal with this for a bitch is to kill the pups herself and get the protein rather than let the pups feed some other threatening animal.