CLEANUP-SYSTEM-DEFINITION-SEARCH-FUNCTIONS attempts to remove SYSDEF-PRELOADED-SYSTEM-SEARCH from the hooks, but it is never added. and right under it, SEARCH-FOR-SYSTEM-DEFINITION also assumes that it's supposed to be called explicitly after the hooks.
i'm afraid i sent this mail too early. the comment above it says:
"Remove known-incompatible sysdef functions from old versions of asdf."
so, if this is indeed a cleanup needed for a proper upgrade, then please ignore my mail and sorry for the noise.