I am using Safari 6.0.1 on OS X 10.8.2 and Safari does not remember my toolbar arrangement or other setting like the default search engine, homepage, etc.
It seems like there is something wrong with your Safari preferences file, try trashing it. (It is located in your
Apple support solved the problem for me. There is nothing wrong with the Safari preference files. In my case the
Try this step by step:
In my case when I reopened Safari it had all the features I had tried to save before without success.
One final important point. The way you select the home page in Safari preferences is to first open Safari in your chosen page, THEN go to Safari preferences and select "Set to current page". For some reason if you type in your chosen page in Preferences it doesn't work.