Sorry I didn't get to answer your first question - I've been busy with non-Yummy stuff for a change.
As you have chosen a bi-directional synchronize, rather than the usual 'Update Server' upload changes method, Yummy performs two synch passes - 1 is local to remote, 2 is remote to local. If you have the 'Compare file size if dates match' option enabled then you can get the situation you've described because there is no way for Yummy to know which file is actually newer.... the remote file size can be different due to differing line endings at the server compared to your local copy, even though the content is actually identical. This can happen if the server is running Windows. for example. I suggest to un-check that option and try again.