Version 4.0 adds an often-requested feature: the refresh setting is no longer global, but instead changes the default refresh setting on new tabs that are opened. You now have the granularity to choose which tabs refresh and which don't (so that you can refresh pages that don't have a meta refresh or asynchronous content, but avoid reloading the ones that take care of their own refreshing/updating). The checkbox for this is on the context menu for each tab. Sorry: there's no way to persist this across browser restarts, other than to choose the default setting that best suits your environment.
Version 4 also (coincidentally) brings in Firefox 4 support, with various tweaks including support for the new Windows Vista/7 Firefox app menu.