Exactly where is the @ sign located? To the immediate right of the patient name or another line?
I'm assuming the patient name being drawn from the header is a field and you are viewing the header area first to enter the name. When you switch back to the document area and the field is automatically populated, you press Ctrl + Shift + J to jump to where you need to begin typing. Word will assume the first letter you type is the beginning of a sentence and capitalize that first word (if you have that option checked in AutoCorrect options). This is normal Word behavior. Without exact examples of when the word is not capitalized, it's impossible to offer any solutions.