■ Common problems in settings persistence

xplorer² by default remembers how it was the last time you used it, and when you restart it next time, it should appear exactly as you left it. That goes for almost all properties like the size and the position of the window, toolbars, pane arrangement, view styles, bookmarks and user commands, color coding etc. As long as you leave the default option Save program state on exit enabled, you won't experience any problems.

The default location for xplorer² settings is the windows registry (the ultimate version can also use a settings file for portability).

Occasionally there are users that have problems with settings. xplorer² seems to develop alzheimer's disease and forget about some settings. This is especially so for view-related properties like the on/off state of color coding, the column set for the detailed view mode and so on. What happens? The problem with a complex system like xplorer² is that there are many different configurations so there are many ways things can go wrong. If you have problems with your settings please go through the following checklist:

Is the default settings persistence enabled? Simple things first: if you untick the default 'save state on exit' in Tools > Options menu (General page) then xplorer² won't save any settings. If you want to save changes, either tick the option or use Actions > Save settings now menu command.
Are you using per-folder settings? xplorer² allows you to save different view settings for particular folders using Actions > Folder settings menu command. This feature is meant to be used exceptionally and for a few folders you always want them seen fixed (e.g. thumbnail view mode for image folders). If you make too many folders special, then confusion may ensue. xplorer² will not save any changes on exit if the last folder you browsed had custom settings saved in it. The solution is to create a new folder somewhere, browse it, then exit xplorer². The fresh folder is certain to be in default state so your settings will be saved.
Scrap containers. These special xplorer² windows have a quirk. If you want your settings saved make sure you have at least one item in the pane when you close the window.
Are you using many folder tabs?. Although you can set each folder tab independently while xplorer² is running, on exit only the active tab (the one selected) saves its settings. When you restart xplorer² you will find all tabs of a pane looking alike. This is a design decision to minimize the size of the settings impact on the registry. The workaround here is to keep on running xplorer² without closing the program — just leave it minimized in the taskbar.
ps. From version 4.0+ tabs can remember their different settings even after a restart
Are you using Layouts?. Each layout (Window menu) has its own settings. If you make changes in one, you won't see them in the other (except for global settings like bookmarks and items under Customize menu). This catches out people opting for replacing windows explorer with xplorer² and opting for a single pane window for integration. This creates a new layout called x2solo. The solution is to avoid using this single window (reinstall if necessary) or customize it separately.
Your bookmarks disappear. You are a victim of your registry cleaner

This list should cover most settings problems — imaginative users may find other unintended ways to knock things off kilter <g>.

If all else fails and you can't persist your settings, you should first close all xplorer² windows (if any) except for one; make all the changes you need in this window and use Actions > Save settings now menu command.