Hi esou,
Have you tried exiting TOAD and temporarily renaming your Formatter options file, which can be located at:
c:\users<username>\AppData\Roaming\Quest Software\Toad for Oracle\12.1\User Files\FmtPlus.opt
This should reset it back to its defaults. If this fixes the problem, then there’s probably something set outside of the Parentheses setting that’s causing this issue (perhaps somewhere in the “List Arrangements” section). I’ve been trying to replicate your issue using my local copy of 12.1, but I haven’t been able to achieve the same results yet.
-John