Duplicate accelerators are not supposed to happen. It is not possible
to set them through the GUI in particular. Nevertheless
gtk_accel_map_load() would apparently let duplicates pass, which could
happen after editing the menurc directly, or using the development
version (no action name migration happens there), or simply after a
potential bug. This is then very annoying because you may see several
actions displaying the same shortcut but only one actually work. And
trying to re-set through GUI the shortcut to the one action you wish to
run does not fix the duplicate issue (you have to laboriously find which
other action use the same accelerator and delete it first).
Better be safe than sorry and make a quick check at startup, then delete
the accelerator on one of the duplicates (you can't guess which one was
actually wanted, but at least you will facilitate manual reset through
the GUI).