Different Wiimote behaviour on connection attempt. 1+2 vs. SYNC

[mbc07]

On BT Passthrough mode (assuming you're using a real Wii BT Adapter), you only have to sync your Wiimotes with the sync button on the battery cover once (make sure a Wii game is running, though, you can't sync otherwise). After this initial syncing, it behaves like on a real console, you just need to press any button on the Wiimote while a game is running and it'll will reconnect automatically. I have no idea of what is causing your other issues, though...