Just updated to SW 2014 and have noticed quite a few buggy things. This one is particularly frustrating since I can't seem to find a work-around yet.
I have an assembly with many parts. I'm trying to do an advanced save-as to just re-name the parts and keep the relations and everything. In 2013, the "specify folder for selected items" bar was empty when you entered the advanced screen. Now, when the advanced screen opens it's filled with a file path of the top level assembly, which immediately changes anything in the references list that does not have that file path.
Notice the green file paths have instantly been changed as soon as this screen is opened.
Without being able to use the Save-As with References function I have to save-as each part individually to keep the references. Painful and time consuming