We adopted our dog in June, also a rescue and after an idyllic summer, things changed. As soon as the eveninge began to get darker, Louie would growl and bark and act in a threatening way every time my husband walked into the room. This lasted throughout the winter and ended as soon as it got lighter in the evenings. A behavourist gave us some suggestions such as rattling a can with coins in to distract him, a water spray bottle, etc. but they were only marginally successful. My husband also took over all feeding and exercising in an effort to increase trust since Louie had no problems with me.
In reality, it was only time (about three years) that resolved the situation and the incredible patience of my husband. I'm sure that anyone else would have returned him to the sanctuary. I should mention too that Louie and my husband were the best of buddys during daylight hours throughout this behaviour.
Not sure if this helps but at least you know someone understands the problem.