It's good she's getting an MRI because that helps you rule out more serious issues sooner rather than later. Continue to be assertive with her doctors! If she does not improve, insist on further tests.
This could be as simple as a vision issue, so be sure that gets checked too.
I am disturbed by this policy of not allowing children to have their parents there unless the children are asleep. What is the point of that? You can't calm and reassure them if they're not awake! Does this apply only to procedures such as MRIs and the reflux, or most of the time? I would push the hospital on exactly how this applies, and I would also tell them you will indeed be with her when she is distressed. If this is a policy that really just means "you can't be in the actual room while an MRI machine is running," that's understandable and is for your safety, but it's not clear to me what the policy actually means. My daughter had an MRI when she had appendicitis, and had an ultrasound too, and I was in the actual room for both procedures.