I still see these "dependency not done" warnings in test-bundle on SBCL and other implementations (I haven't checked them all, but at least my big three: SBCL, Allegro, and CCL).

Running test-bundle.script with sbcl-1.4.3-macosx-x64
; loading #P"/Users/rpg/lisp/asdf/test/test-bundle.script"
; Registering system test-asdf
;; loading #P"/Users/rpg/lisp/asdf/test/test-asdf.asd"
TEST-BUNDLE
  ASDF-TEST::*BUNDLE-1* => #P"/Users/rpg/lisp/asdf/build/fasls/sbcl-1.4.3-macosx-x64/asdf/test/test-asdf/bundle-1--system.fasl"
  ASDF-TEST::*BUNDLE-2* => #P"/Users/rpg/lisp/asdf/build/fasls/sbcl-1.4.3-macosx-x64/asdf/test/test-asdf/bundle-2--system.fasl"
;; loading #P"/Users/rpg/lisp/asdf/build/fasls/sbcl-1.4.3-macosx-x64/asdf/test/test-asdf/bundle-1--system.fasl"
WARNING:
   Computing just-done stamp  for action (LOAD-OP
                                          "test-asdf/bundle-1"), but dependency (LOAD-OP
                                                                                 "test-asdf/bundle-1"
                                                                                 "file1") wasn't done yet!
WARNING:
   Computing just-done stamp  for action (LOAD-OP
                                          "test-asdf/bundle-1"), but dependency (LOAD-OP
                                                                                 "test-asdf/bundle-1"
                                                                                 "file3") wasn't done yet!
WARNING:
   Computing just-done stamp  for action (LOAD-OP
                                          "test-asdf/bundle-1"), but dependency (COMPILE-OP
                                                                                 "test-asdf/bundle-1") wasn't done yet!
;; loading #P"/Users/rpg/lisp/asdf/build/fasls/sbcl-1.4.3-macosx-x64/asdf/test/file1.fasl"
;; loading #P"/Users/rpg/lisp/asdf/build/fasls/sbcl-1.4.3-macosx-x64/asdf/test/file3.fasl"
;; loading #P"/Users/rpg/lisp/asdf/build/fasls/sbcl-1.4.3-macosx-x64/asdf/test/test-asdf/bundle-2--system.fasl"
WARNING:
   Computing just-done stamp  for action (LOAD-OP
                                          "test-asdf/bundle-2"), but dependency (LOAD-OP
                                                                                 "test-asdf/bundle-2"
                                                                                 "file2") wasn't done yet!
WARNING:
   Computing just-done stamp  for action (LOAD-OP
                                          "test-asdf/bundle-2"), but dependency (COMPILE-OP
                                                                                 "test-asdf/bundle-2") wasn't done yet!

This seems like a bug somewhere, right? And it must be an ASDF bug, probably in the definition of LOAD-OP for bundles.

So, even after the last email, I'm inclined to hold up a release until I understand this bug and kill it.