If Rhino is unable to save any edits to your toolbar layout (the original default keeps coming back after you close and reopen Rhino) you may have a problem with Windows' file-writing permissions. See this page for some suggestions on how to test/fix this.
Note: always edit your toolbar layout with only one instance of Rhino open, otherwise your edits may be wiped out (overwritten) by another unmodified instance of Rhino closing.
If one day you open Rhino and all your toolbars are gone, don't panic! There is usually a simple solution to get them back.
If your toolbars are doing a constant disappearing act, though, there is something else wrong, contact McNeel support with your problem.
Problem with toolbar layouts not sticking and docking correctly in Rhino V3
The utility deletes the following key in the registry to make Rhino “forget” some settings that make the toolbars not dock correctly: HKEY_CURRENT_USER\Software\McNeel\Rhinoceros\3.0\Scheme: Default\Control bar manager