These settings configure the behaviour of refreshing the file system.
By Manual Refresh you can configure how the manual Refresh by View|Refresh (see Directory Tree and File Table) behaves. All options take into account the scanned/unscanned state of the working copy, see Refresh/Scan.
You have the option to refresh Always root directory. In this case the directory selection in the tree does not matter, but always the whole project is refreshed. This option requires the most effort, but will guarantee that after changing the selection in the tree, displayed data is still up to date (relative to the last refresh time).
You can also choose to refresh only the Selected directory recursively. This option can be useful, if you know, that you are only working a specific part of your whole SVN project.
The option Selected directory (recursively if set for view) also refreshes only the selected directory. Whether this refresh is recursive or not, depends on if View|Files From Subdirectories is selected. This option is the fastest way of refreshing as it is most selective, but it requires you to be always aware of which directories you have refreshed and hence which information displayed in directory tree and file table are actually up to date.
Scrolling specifies whether to Scroll to top of table or Try to keep same files visible.
SmartSVN can also automatically perform a refresh of the project after it gets the focus back, if configured by Refresh on frame activation. The automatic refresh behaves the same way as configured for the Manual Refresh. It can be useful if you are working some time on your project (e.g. in an IDE), then decide to check and commit your changes and hence get back to SmartSVN.
You have either the option to disable automatic refresh by Never, have an immediate refresh by Immediately or have only a refresh, if SmartSVN has been inactive for at least 5 seconds by After more than 5 seconds of deactivation. This option is useful, if you typically switch to other applications for a short period of time and do not want to trigger automatic refresh. This last option is only available on non-Windows platforms, as on windows as special native module is used, which makes the refresh more efficient and will only refresh if necessary.