I use Visual Assist X ver. 10.4.1635.1 built 2008.04.18 on Visual Studio 2008. The problem is that my custom setting of VA are not saved - each time I reopen the Studio, the settings of VA are back to defaults.
Can you make sure there is only one open instance of Visual Studio. The last instance of VS2008 that gets closed saves out its settings, overwriting any earlier settings.
You might want to try running Process Monitor, and set it to only show registry activity from "devenv.exe" and see if this offers any clues: