nothing has been changed around synching, so if it was working ok before and suddenly started taking a long time then you might consider what has changed on your phone.
You dont say what type of phone but if its synched using MTP mode, i myself occasionally experience random initial slowness and then other times its really fast but there is no reason i have every found for it on the MusicBee side. If its MSC mode i really think the problem will be with the device