Link2sd not working properly
Stock Samsung software always mounts the SD card after the system is up, at least on my Vibrant, so I would expect there's not too much you can do about that without hacking the startup scripts (presumably difficult).

As for the second problem, the Market description says: "It can break some apps if they are not meant to be moved to the SD card (Such as Widgets)."  Try moving any widgets back to your phone storage.