I've run prelink now on 2 different shrike desktop systems, trying various options, and on each system it causes the identical flakiness. One thing in particular I noted on both systems was that after prelinking, the gnome logout button is broken - it has no effect, so that CTRL-ALT-BKSP must be used to exit.
I can't reproduce that. I've prelinked one system which was upgraded from RHL 8, and one system that was a fresh install with GNOME, KDE, and development packages. Neither seems to have any problems, including logging out.
I tried each of the following:
prelink -av prelink -avmR prelink -avm --libs-only
I just used prelink -am