Why is the email address different when I reply to one of the messages sent by the customer on the transaction record?

Most likely the customer replied to an email generated via the To be Emailed field and the email populated in there was not of the customer's on the transaction record. The From field of the message record generated from the reply will look like this:

From: Customer Name (*email address on the To be Emailed field)

When you click on the Reply button the Recipients tab wll look like this:

Recipient: Customer Name
Email Address: *email address on the customer record

The reason why the Email Address changes when you click on the Reply button is because the system populates the Recipient field with the Name found at From field of the message instead of the email address.