It seems like the old way of updating used in both Clickable Maps and BOB doesn't work on all systems any more (especially mine
It is a new thing, I just installed an older version and it's suffering from the same problem, even though at that time there were no errors.
It used to open a window, load the URL of UserScripts and close the window directly. This would create a popup about installing the script, which didn't disappear when closing the window. Now it does disappear when closing the window on some systems, and since it's done immediately.. No way to update through that any more.
Switching to a simpler mechanism now, but I'll have to tell people to upgrade through a link.
If someone uses the same mechanism, it might be good to change it.