You did not indicate the release your using since 7.9.X and VX releases work a little differently in this area. Also, you did not say what objects on the user layer that are not updated.
However commonly when I have seen this issue it has to do with Text strings. by default xPCB will retain Text locations when cells are updated in layout based on library changes. This is to ensure the work done to improve the text locations for RefDes and Drawings that are instance specific do not get wiped out during an update. For text you must open ECO->Replace Cell and do a reset with the option "Keep text attributers during replace" deselected.
i using VX 1.1 run on windows7 64 bit
for example :
change user layer name in central library cell - it's not update in board layout.
change refdes text line width.