I'm using Glims to switch Safari's search engine to DuckDuckGo, and have been having two odd back-button issues that seem to be Glims' fault.
The more annoying one is that if I open a new (empty) window, do a search via the Glims-modded search field, and click a link in the results list, some percentage of the time the back button does not work--the search results page is not in the history stack.
The other problem (probably related) is that if I right click a search-result link or two and open them in another tab in the background, then try to regular-click a search result link to open it in the main window (basically, I want to view three results pages, so I open two in new tabs then the third in the results tab), the regular-click doesn't register--I can only open links if I right-click and open them in new tabs.
It's tremendously annoying, and the behavior has been more or less the same, albeit somewhat erratic, on both 10.7 and 10.8, Safari 5 and Safari 6. I assume it's not DuckDuckGo's fault, since they don't seem to be doing anything exotic code-wise, although it's possible it is.