After clearing a reading list, the sorting of calibre is messed up by the plugin, with books from the last displayed list (marked by the plugin) are pushed to the bottom of the view. This happens because the plugin modifies calibre's sort to be based on the marked field.
The version attached to this post fixes this problem by restoring calibre's sort to its original state after a reading list is cleared.
There is only one case in which the sorting will not be restored, under calibre versions <= 5.43, it happens if the user switches to another library while a reading list is still in display. Thanks to Kovid,
this is taken care of in future calibre versions.