Why is my postmaster process (sometimes) becoming unmanageable after a WAL base restore?
In general if you are seeing problems of this sort, it may be best to take them up on the pgsql-bugs list.  People there can help figure out what information to gather to help determine what the scope of this misbehavior is and help fix it for you.

Also 8.4.11 to 8.4.12 wal restore should work just fine.

If this is only occasionally happening, I don't think your explanations get there.  It sounds like something that really could use additional troubleshooting by people who can determine if a code fix is required.