I've compiles a crude applescript workaround to deal with the problem until its solved:
Copy and paste this into a new Applescript editor document and save as an app.... and let it run all the time... it'll check and apply rules every 2 minutes.... as long as you don't press on a key or click something when its doing its series of keystrokes, and the only way to quit it is to force quit. As I said, its crude, but it works for me.
tell application "Finder"
tell application "Mail"
set a to 0
repeat with theAccount in (every account)
repeat with theBox in (every mailbox of theAccount)
set a to a + (count (messages in theBox where read status is false))
end repeat
end repeat
end tell
if a is not 0 then
tell application "Mail" to try
tell message viewer 1 to set selected messages to {first message of beginning of (get selected mailboxes) whose read status is false}
activate
end try
tell application "Mail"
activate
end tell
tell application "System Events"
key code 120 using control down
keystroke tab
keystroke tab
keystroke tab
keystroke tab
keystroke tab
keystroke tab
keystroke space
repeat 12 times
delay 0.1
key code 125
end repeat
delay 1
keystroke space
end tell
end if
delay 60 * 2
end tell
