Steps to reproduce the issue:
Go to View | Toad options | Formatter and, on the right panel , select “Oracle Formatter Options” | Header
Select “Enable“
Write a header with two lines. For example:
My Header
Company Name
Click Apply and Ok
The second line is not saved. You can see this by opening the Header option again (you will see there just “My Header” or by formatting a select as the header will be just the first line:
/* Formatted on 17/05/2017 11:44:13 (QP5 v5.312) My Header */
WORKAROUND
Please type all the header in a single line
STATUS
Waiting for fix in a future release of Toad for Oracle