The synchronization profile shouldn't be related to the shuffle mode.

On the other hand, if you've set your synch profile to cycle different tunes and artists into your player each time you dock it, then you might be seeing a side-effect of that. For instance, if you have told it to delete artists you've recently listened to and insert artists from the PC that you haven't heard in a while, then it might have fewer tunes on the player than you think.