On my Tarmac Pro (58") I noticed some noise when using 39x25. The chain does not rub against the front derailleur and the rear derailleur seams to be correctly aligned with the sprocket. Is it normal?

Seems kinda strange that it would make noise in that gear combo as its not a extreme to extreme combo. For example on my Tarmac Comp if it have it in the big ring up front and back, well lets just say you dont ride that way for very long. Check out your drive train and adjust it up good, or take it to your LBS if your more comfortable there.