It’s entirely possible that she may not be uncomfortable with being petted! Remember, as humans, we have this tendency to interpret big wide-open eyes as being sad or emotional. There’s science, though, that points out that dogs we’re bonded with actually get an oxytocin boost from gazing into our eyes. So next time she does that, look at the rest of her face and her behavior to figure out what’s going on. If the skin around her face is still fairly relaxed and her posture is loose, and she’s actively gazing into your eyes, it’s probably a positive interaction for her!
As to why she pauses wagging and stands still, I can’t say. I’ve definitely seen some dogs who stop wiggling when you pet them but still enjoy the interaction. Maybe it’s a way to more thoroughly enjoy the contact, who knows. The best way to check is to pause with your petting but still offer your hand. If the dog chooses to re-engage by nudging your hand or bumping their body into your or anything similar, that means keep petting.