Please manually load the new xml format options file in the formatter options windows. This should solve the problem.
WORKAROUND:
1. Open Tools | Formatter Tools | Formatting Options;
2. Click Open button and select FmtOptions.opt.xml to load it into the formatter;
3. Verify the options after loading;
4. Close formatter options windows and now all options should work as expected.
STATUS:
Waiting for fix in a future release of SQL Navigator for Oracle
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