I finally called in to fix this issue. Turns out when you're waitlisted for an upgrade using RPU (perhaps other instruments) the sked update only changes the reserved coach seat, but not the WL segment in C.

This means that you can only get upgraded from a WL, with a sked change, if you call in and have an agent manually resync the WL to include the sked change. Just accepting the change on .bomb doesn't update the WL segment. And since it's no longer in sync with the flight sked, if R space opened, you won't get upgraded.

Has this glitch in SHARES been noted before?