When upgrading to version 9.7, the formatting options that were set in a prior version of Toad do not format the same way in version 9.7. This happens whether version 9.7 is installed over the previous version or if version 9.7 is installed along side the old version and the older version's FmtPlus.opt file is copied over to version 9.7.
The code Formatting component, "Formatter Plus" has been replaced with "QP5 Formatter" in version 9.7. QP5 will provide support for 10g and 11g syntax as well as additional support for more complex statements. The new formatter also allows us to support future Oracle syntax as new versions are released. While the Formatter options window looks very similar, there are some differences. QP5 formatter will no longer behave exactly like Formatter plus. Running diffs with code formatted by Formatter Plus against code formatted by QP5 will result in differences just about every time. We suggest checking all source code out, re-formatting it with the new formatter, then checking it back in again. This will provide a point in time, one check-in version, which is only for the new formatter. Future diffs won't be affected. QP5 formatting will also be slower, noticeably slower while formating very large files or large sets of files. This is a known issue and performance will increase in future versions.
Adjust the formatting options in version 9.7 manually to get them to their desired states. The formatter options can be found by selecting View | Formatter Options in Toad's menu bar. If needed, there is a table in the help menu to show where some of the options have been moved to in the new version. You can find the table by searching 'Formatter Options' in Help.